Cbcb - User contributions [en]

https://wiki.umiacs.umd.edu/cbcb/api.php?action=feedcontributions&feedformat=atom&user=Cmhill Cbcb - User contributions [en] 2026-04-12T18:06:07Z User contributions MediaWiki 1.43.7 https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5688 Partition 2009-08-27T21:23:45Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M<br /> <br /> If the first row of the metadata file does not contain the column information, then specify a separate column header file with '''-c [file]'''.<br /> <br /> The format of a *.re file changes slightly with the addition of the metadata file. In addition to specifying the regexp, a '''category''' field must also be added to specify which column the regexp will be checked against.<br /> <br /> To populate the xml file with the metadata information and split a given fasta file:<br /> ./Partition.py -b [input.re] -f [input.fasta] -m [metadata.map] -s [dir/output]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5687 Partition 2009-08-27T20:44:40Z

<p>Cmhill: /* Use a metadata file to populate the partitions. */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M<br /> <br /> If the first row of the metadata file does not contain the column information, then specify a separate column header file with '''-c [file]'''.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5686 Partition 2009-08-27T20:44:33Z

<p>Cmhill: /* Use a metadata file to populate the partitions. */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M<br /> <br /> If the first row of the metadata file does not contain the column information, then specify a separate column header file with ''-c [file]''.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5685 Partition 2009-08-27T20:44:25Z

<p>Cmhill: /* Use a metadata file to populate the partitions. */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M<br /> <br /> If the first row of the metadata file does not contain the column information, then specify a separate column header file with '-c [file]'.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5684 Partition 2009-08-27T20:43:39Z

<p>Cmhill: /* Use a metadata file to populate the partitions. */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M<br /> <br /> If the first row of the metadata file does not contain the column information, then specify a separate column header file with =-c [file]=.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5683 Partition 2009-08-27T20:43:23Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M<br /> <br /> If the first row of the metadata file does not contain the column information, then specify a separate column header file with **-c [file]**.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5682 Partition 2009-08-27T20:35:09Z

<p>Cmhill: /* Use a metadata file to populate the partitions. */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M<br /> <br /> If the first row of the metadata file does not contain the column information, then specify a separate column header file with *-c [file]*</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5681 Partition 2009-08-27T20:20:50Z

<p>Cmhill: /* Use a metadata file to populate the partitions. */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5680 Partition 2009-08-27T20:20:23Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===<br /> A metadata file is a file that contains information about a set of sequences.<br /> #SampleID LRHand Sex <br /> S1 R F <br /> S2 L M</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5575 Partition 2009-08-13T18:57:37Z

<p>Cmhill: /* Use a file of metadata that will be used to populate the partitions. */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a metadata file to populate the partitions.===</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5574 Partition 2009-08-13T18:57:18Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.<br /> ===Use a file of metadata that will be used to populate the partitions.===</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5573 Partition 2009-08-13T18:30:42Z

<p>Cmhill: /* Given the input file, build and populate a partition */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o dir/file]<br /> <br /> The -o option specifies if the user wants to save the partition file as something other than the default temppart.xml.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5567 Partition 2009-08-13T15:47:40Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).<br /> ===Given the input file, build and populate a partition===<br /> ./Partition.py -b [input.re] -f [input.fasta] [-o output/dir]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5564 Partition 2009-08-13T14:53:44Z

<p>Cmhill: /* Format of an input regular expression (*.re) file */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of the *.re input file is:<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> where [name] represents the name of the partition, and the key-value pairs will represent the attributes.<br /> <br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5563 Partition 2009-08-13T14:52:50Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of an input regular expression (*.re) file===<br /> The format of an<br /> [name]<br /> key1 = value1<br /> key2 = value2<br /> ...<br /> [name2]<br /> key1 = value1<br /> ...<br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...<br /> Using the format above, the partition can only have two levels. It is possible to have multiple levels, but the input file needs to be an xml file (explained below).</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5562 Partition 2009-08-13T14:33:27Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ===Options===<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of a input regular expression (*.re) file===<br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5561 Partition 2009-08-13T14:33:05Z

<p>Cmhill: /* Format of a input regular expression (*.re) file */</p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> '''Options'''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of a input regular expression (*.re) file===<br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = a.*<br /> [B]<br /> info = animals that start with B<br /> regexp = b.*<br /> ...</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5560 Partition 2009-08-13T14:32:46Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> '''Options'''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of a input regular expression (*.re) file===<br /> Example of an input file that clusters animals by their first letter:<br /> [animals]<br /> info = all animals<br /> [A]<br /> info = animals that start with A<br /> regexp = [Aa].*<br /> [B]<br /> info = animals that start with B<br /> regexp = [Bb].*<br /> ...</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5559 Partition 2009-08-13T14:14:55Z

<p>Cmhill: </p> <hr /> <div>==Summary==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> '''Options'''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> ==Tutorial==<br /> ===Format of a input regular expression (*.re) file===</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5558 Partition 2009-08-13T14:14:09Z

<p>Cmhill: </p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ''' Options '''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> == Tutorial ==<br /> === Format of a input regular expression (*.re) file ===</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5557 Partition 2009-08-13T14:13:19Z

<p>Cmhill: /* Tutorial */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ''' Options '''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> == Tutorial ==<br /> ''' Format of a input regular expression (*.re) file '''</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5556 Partition 2009-08-13T14:13:10Z

<p>Cmhill: /* Tutorial */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ''' Options '''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> === Tutorial ===<br /> ''' Format of a input regular expression (*.re) file '''</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5555 Partition 2009-08-13T14:11:45Z

<p>Cmhill: </p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ''' Options '''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre><br /> <br /> == Tutorial ==<br /> ''' Format of a input regular expression (*.re) file '''</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5554 Partition 2009-08-13T14:10:28Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> ''' Options '''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre></div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5553 Partition 2009-08-13T14:10:11Z

<p>Cmhill: </p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> '' Options ''<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre></div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5552 Partition 2009-08-13T14:09:42Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest, but possibly unstable builds''']<br /> <br /> == Options ==<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre></div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5551 Partition 2009-08-13T14:09:24Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> /fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest but possibly unstable builds''']<br /> <br /> == Options ==<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre></div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5550 Partition 2009-08-13T14:08:42Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> <pre>/fs/szasmg/metagenomics/Partition/Partition.py ['''stable''']<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py ['''latest but possibly unstable builds''']</pre><br /> <br /> == Options ==<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre></div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5549 Partition 2009-08-13T14:08:08Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> <pre>/fs/szasmg/metagenomics/Partition/Partition.py [stable]<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]</pre><br /> <br /> == Options ==<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre></div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5548 Partition 2009-08-13T14:07:47Z

<p>Cmhill: </p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> <pre>/fs/szasmg/metagenomics/Partition/Partition.py [latest stable]<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]</pre><br /> == Options ==<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre></div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5547 Partition 2009-08-13T14:07:06Z

<p>Cmhill: </p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> */fs/szasmg/metagenomics/Partition/Partition.py [latest stable]<br /> */fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]<br /> == Options ==<br /> <pre><br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.<br /> </pre></div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5546 Partition 2009-08-13T14:04:06Z

<p>Cmhill: /* Options */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> */fs/szasmg/metagenomics/Partition/Partition.py [latest stable]<br /> */fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]<br /> == Options ==<br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5545 Partition 2009-08-13T14:03:54Z

<p>Cmhill: /* Options */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> */fs/szasmg/metagenomics/Partition/Partition.py [latest stable]<br /> */fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]<br /> == Options ==<br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information<br /> for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5544 Partition 2009-08-13T14:03:33Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> */fs/szasmg/metagenomics/Partition/Partition.py [latest stable]<br /> */fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]<br /> == Options ==<br /> -p Populate the given partition/XML.<br /> -b Given the input file, build a partition.<br /> -m Metadata file that will be used to populate the partitions.<br /> -h Header information for the metadata, if not present column information<br /> for metadata will be found in first line of the metadata.<br /> -f Input fasta file.<br /> -s Split the fasta file based on the partition information<br /> and output to the directory.<br /> -o Name of the output .part file.<br /> -c Convert an old partition format into the new xml format.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5543 Partition 2009-08-13T14:02:31Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> */fs/szasmg/metagenomics/Partition/Partition.py [latest stable]<br /> */fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5542 Partition 2009-08-13T13:51:25Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> **/fs/szasmg/metagenomics/Partition/Partition.py**<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5541 Partition 2009-08-13T13:51:07Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> '/fs/szasmg/metagenomics/Partition/Partition.py'<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5540 Partition 2009-08-13T13:50:16Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> *<br /> /fs/szasmg/metagenomics/Partition/Partition.py<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5539 Partition 2009-08-13T13:49:59Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> */fs/szasmg/metagenomics/Partition/Partition.py*<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5538 Partition 2009-08-13T13:49:51Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file. Partition.py is located at:<br /> */fs/szasmg/metagenomics/Partition/Partition.py<br /> /fs/szasmg/metagenomics/Partition/MetaPart/src/Partition.py [latest but possibly unstable builds]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5537 Partition 2009-08-13T13:47:06Z

<p>Cmhill: /* Summary */</p> <hr /> <div>== Summary ==<br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5536 Partition 2009-08-13T13:46:53Z

<p>Cmhill: </p> <hr /> <div>== Summary ==<br /> <br /> Partition is a python script that takes an input of regular expressions and metadata to build an xml file of matching header information from a fasta-formatted file.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Partition&diff=5522 Partition 2009-08-10T14:59:44Z

<p>Cmhill: </p> <hr /> <div>Testing.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Software&diff=5521 Cbcb:Pop-Lab:Software 2009-08-10T14:59:35Z

<p>Cmhill: /* Software developed by members of our group */</p> <hr /> <div>==Software developed by members of our group==<br /> [http://amos.sourceforge.net AMOS] - open-source assembly package <br><br /> [http://amos.sourceforge.net/docs/bambus Bambus] - hierachical genome scaffolder <br><br /> [http://amos.sourceforge.net/Figaro Figaro] - sequence trimmer that does not require knowledge about the vector sequence <br><br /> [http://www.cbcb.umd.edu/~whitej/metastats/detection.shtml MetaStats] - statistical methods for comparing metagenomic samples <br><br /> [http://www.cbcb.umd.edu/soma On-Soma] - scaffolder for optical mapping data <br><br /> [http://ardb.cbcb.umd.edu ARDB] - antibiotic resistance database <br><br /> [http://bowtie-bio.sourceforge.net Bowtie] - ultrafast and memory-efficient short read aligner<br><br /> Prokaryotic annotation pipeline <br><br /> Comparative annotation viewer <br><br /> [[Partition]]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Partition&diff=5520 Cbcb:Pop-Lab:Partition 2009-08-10T14:59:21Z

<p>Cmhill: </p> <hr /> <div>Testing.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Software&diff=5519 Cbcb:Pop-Lab:Software 2009-08-10T14:59:14Z

<p>Cmhill: /* Software developed by members of our group */</p> <hr /> <div>==Software developed by members of our group==<br /> [http://amos.sourceforge.net AMOS] - open-source assembly package <br><br /> [http://amos.sourceforge.net/docs/bambus Bambus] - hierachical genome scaffolder <br><br /> [http://amos.sourceforge.net/Figaro Figaro] - sequence trimmer that does not require knowledge about the vector sequence <br><br /> [http://www.cbcb.umd.edu/~whitej/metastats/detection.shtml MetaStats] - statistical methods for comparing metagenomic samples <br><br /> [http://www.cbcb.umd.edu/soma On-Soma] - scaffolder for optical mapping data <br><br /> [http://ardb.cbcb.umd.edu ARDB] - antibiotic resistance database <br><br /> [http://bowtie-bio.sourceforge.net Bowtie] - ultrafast and memory-efficient short read aligner<br><br /> Prokaryotic annotation pipeline <br><br /> Comparative annotation viewer <br><br /> [[Cbcb:Pop-Lab:Partition]]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:How_to_use_the_partition_software%3F&diff=5518 Cbcb:Pop-Lab:How to use the partition software? 2009-08-10T01:31:13Z

<p>Cmhill: </p> <hr /> <div>Testing.</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:How-to&diff=5517 Cbcb:Pop-Lab:How-to 2009-08-10T01:31:06Z

<p>Cmhill: /* How-To repository */</p> <hr /> <div>==How-To repository==<br /> [http://www.cbcb.umd.edu/intranet/resources.shtml Getting started at the CBCB] <br><br /> [[Cbcb:Pop-Lab:AMOS-CVS How to use AMOS through CVS]] <br><br /> [[Cbcb:Pop-Lab:AMOScmp-SR How to use AMOScmp with short read data ]] <br><br /> How do I annotate a genome at the CBCB?<br><br /> [[Cbcb:Pop-Lab:How do I run the new Bambus | How do I run the new Bambus?]] <br><br /> How do I use the antibiotic resistance database?<br><br /> How do I use the antibiotic resistance database locally? <br><br /> How do I run jobs on the grid? <br><br /> [[Cbcb:Pop-Lab:OTUs How do I create OTUs from 16S rRNA sequence data? | How do I create OTUs from 16S rRNA sequence data?]] <br><br /> How do I compare metagenomic datasets through the metastats website?<br><br /> How do I compare metagenomic datasets using R directly? <br><br /> How do I find CRISPRs in a new genome?<br><br /> [[Cbcb:Pop-Lab:SOMA How do I scaffold a genome using optical maps (both locally and through the web) ]] <br><br /> How do I generate graph information out of Minimus?<br><br /> What tools are available for doing <i>in silico</i> finishing at the CBCB? <br><br /> How do I generate a scaffold graph starting from a 454 .ace file?<br><br /> How do I draw a pretty picture of a scaffold stored in an AMOS bank?<br><br /> [[Cbcb:Pop-Lab:How to use the partition software? | How do I use the partition software?]]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Chris-Report&diff=5379 Cbcb:Pop-Lab:Chris-Report 2009-06-13T00:47:18Z

<p>Cmhill: /* Tasks */</p> <hr /> <div>== June 12, 2009 ==<br /> ===Tasks===<br /> '''Intergenic space and gene ontology work'''<br /> *Investigated GO annotation tools that Bo has linked me to.<br /> *I have been working on the Snail, ''Lottia gigantea'', genome.<br /> *Found the top 10% intergenic space with relative ease, however there was no GO annotation file for the genes. Most of the genomes of interest will not have a GO annotation file (shocker, I know).<br /> *BLAST'd the sequences using Blast2GO, '''ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.''' http://www.blast2go.org/<br /> *Blast2GO has a pipeline version, so I have been planning a way to take new incomplete genomes and have them run through this annotation pipeline.<br /> *BLAST took around 8 hours for ~2200 sequences using an online database. I will run another group on the CBCB's BLAST.<br /> *GO annotation using Blast2GO took around 24 hours.<br /> *I plan on running HMMs for the approximate 200 sequences with no suitable hits this weekend.<br /> '''Partition'''<br /> *Drastically overhauling the backend of my partition program to make it more extendable/robust.<br /> *Adding XML support to make parsing easier and increase possible functionality.<br /> *Need to focus on getting James something usable asap.<br /> <br /> ===Summer Goals===<br /> *Finish analyzing the intergenic space of the incomplete genomes. Determine future possibilities/publications.<br /> *Modify/extend partition program to incorporate into James' metagenomic pipeline.<br /> *Include viral metagenomic data into GeneParser. <br /> <br /> == Mar 2, 2009 ==<br /> ===Tasks===<br /> '''Intergenic space and gene ontology work with Cristian''' <br /> *Approach<br /> Get the gene-spacing information - typically a simple parse of GFF files, if they are available.<br /> Get the gene function information - use GO if available.<br /> Rank the genes based on 5' spacing size.<br /> Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge<br /> *Completed genomes<br /> **Anenome, ''Nematostella vectensis''<br /> **Frog, ''Xenopus tropicalis''<br /> **Waterflea, ''Daphnia pulex''<br /> *Incomplete genomes that require blast<br /> **Gastropod Snail, ''Lottia gigantea''<br /> **Polychaete Worm, ''Capitella sp''<br /> *Future genomes<br /> **Leech, ''Helobdella robusta''<br /> **Flatworm (Planaria), '' Schmidtea mediterranea'' <br /> **Sea Slug,'' Aplysia californica''<br /> **Snail,'' Biomphalaria glabrata''<br /> **Slime-mold, ''Dictyostelium purpureum QSDP1''<br /> *Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes.<br /> <br /> '''Partitioning System'''<br /> *Splitting contigs based on "subgroup" information - essentially extending breaking up an entire assembly into multiple "sub-assemblies" each containing just reads from a single subgroup.<br /> <br /> '''Conserved genomic elements in bacteria'''<br /> *Update elements based on Adam's changes to Insignia.<br /> *Find something to write about.<br /> ===Interesting Stuff===<br /> *New insights into aging based on transcription factors, [http://med.stanford.edu/news_releases/2008/july/aging-worm.html Prevailing theory of aging challenged in Stanford worm study]</div>

Cmhill https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Chris-Report&diff=5378 Cbcb:Pop-Lab:Chris-Report 2009-06-13T00:45:46Z

<p>Cmhill: /* Tasks */</p> <hr /> <div>== June 12, 2009 ==<br /> ===Tasks===<br /> '''Intergenic space and gene ontology work'''<br /> *Investigated GO annotation tools that Bo has linked me to.<br /> *I have been working on the Snail, ''Lottia gigantea'', genome.<br /> *Found the top 10% intergenic space with relative easy, however there was no GO annotation file for the genes. <br /> *BLAST'd the sequences using Blast2GO, '''ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.''' http://www.blast2go.org/<br /> *Blast2GO has a pipeline version, so I have been planning a way to take new incomplete genomes and have them run through this annotation pipeline.<br /> *BLAST took around 8 hours for ~2200 sequences using an online database. I will run another group on the CBCB's BLAST.<br /> *GO annotation using Blast2GO took around 24 hours.<br /> *I plan on running HMMs for the approximate 200 sequences with no suitable hits this weekend.<br /> '''Partition'''<br /> *Drastically overhauling the backend of my partition program to make it more extendable/robust.<br /> *Adding XML support to make parsing easier and increase possible functionality.<br /> *Need to focus on getting James something usable asap.<br /> <br /> ===Summer Goals===<br /> *Finish analyzing the intergenic space of the incomplete genomes. Determine future possibilities/publications.<br /> *Modify/extend partition program to incorporate into James' metagenomic pipeline.<br /> *Include viral metagenomic data into GeneParser. <br /> <br /> == Mar 2, 2009 ==<br /> ===Tasks===<br /> '''Intergenic space and gene ontology work with Cristian''' <br /> *Approach<br /> Get the gene-spacing information - typically a simple parse of GFF files, if they are available.<br /> Get the gene function information - use GO if available.<br /> Rank the genes based on 5' spacing size.<br /> Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge<br /> *Completed genomes<br /> **Anenome, ''Nematostella vectensis''<br /> **Frog, ''Xenopus tropicalis''<br /> **Waterflea, ''Daphnia pulex''<br /> *Incomplete genomes that require blast<br /> **Gastropod Snail, ''Lottia gigantea''<br /> **Polychaete Worm, ''Capitella sp''<br /> *Future genomes<br /> **Leech, ''Helobdella robusta''<br /> **Flatworm (Planaria), '' Schmidtea mediterranea'' <br /> **Sea Slug,'' Aplysia californica''<br /> **Snail,'' Biomphalaria glabrata''<br /> **Slime-mold, ''Dictyostelium purpureum QSDP1''<br /> *Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes.<br /> <br /> '''Partitioning System'''<br /> *Splitting contigs based on "subgroup" information - essentially extending breaking up an entire assembly into multiple "sub-assemblies" each containing just reads from a single subgroup.<br /> <br /> '''Conserved genomic elements in bacteria'''<br /> *Update elements based on Adam's changes to Insignia.<br /> *Find something to write about.<br /> ===Interesting Stuff===<br /> *New insights into aging based on transcription factors, [http://med.stanford.edu/news_releases/2008/july/aging-worm.html Prevailing theory of aging challenged in Stanford worm study]</div>

Cmhill