Dpuiu Perl - Revision history

Dpuiu: /* Useful modules */

2011-04-21T20:32:45Z

Useful modules

← Older revision		Revision as of 20:32, 21 April 2011
Line 210:		Line 210:

	git clone git://github.com/bioperl/bioperl-ext.git		git clone git://github.com/bioperl/bioperl-ext.git
	perl Makefile.PL PREFIX=/fs/szdevel/core-cbcb-software/Linux-x86_64		perl Makefile.PL PREFIX=/fs/szdevel/core-cbcb-software/Linux-x86_64 "DIR=Bio/Ext Bio/SeqIO/staden"
	make		make
	make test		make test
	make install		make install

			mv Makefile Makefile.old
			mv ./Bio/Ext/Align/Makefile ./Bio/Ext/Align/Makefile.old
			mv ./Bio/SeqIO/staden/Makefile ./Bio/SeqIO/staden/Makefile.old

	#if error ...		#if error ...
	~~make clean~~
	cat Makefile.old \| p 'if(/^(\w+FLAGS\s+=)(.+)/) { print $1," -fPIC ",$2,"\n" } else { print $_ }' > Makefile		cat Makefile.old \| p 'if(/^(\w+FLAGS\s+=)(.+)/) { print $1," -fPIC ",$2,"\n" } else { print $_ }' > Makefile
	cat ./Bio/Ext/Align/Makefile.old \| p 'if(/^(\w+FLAGS\s+=)(.+)/) { print $1," -fPIC ",$2,"\n" } else { print $_ }' > ./Bio/Ext/Align/Makefile		cat ./Bio/Ext/Align/Makefile.old \| p 'if(/^(\w+FLAGS\s+=)(.+)/) { print $1," -fPIC ",$2,"\n" } else { print $_ }' > ./Bio/Ext/Align/Makefile
	cat ./Bio/SeqIO/staden/Makefile.old \| p 'if(/^(\w+FLAGS\s+=)(.+)/) { print $1," -fPIC ",$2,"\n" } else { print $_ }' > ./Bio/SeqIO/staden/Makefile		cat ./Bio/SeqIO/staden/Makefile.old \| p 'if(/^(\w+FLAGS\s+=)(.+)/) { print $1," -fPIC ",$2,"\n" } else { print $_ }' > ./Bio/SeqIO/staden/Makefile

			TO_INST_PM

	= Variables =		= Variables =

2011-04-21T18:42:41Z

Modules

@@ Line 193: / Line 193: @@
 * File::Find
 * [http://bonsai.hgc.jp/~mdehoon/software/cluster/cluster.pdf Algorithm::Cluster]
 = Variables =

2011-03-03T21:24:17Z

Modules

← Older revision		Revision as of 21:24, 3 March 2011
Line 189:		Line 189:
	$ ./Build install		$ ./Build install

	Useful ~~ones:~~		== Useful modules ==
	* [http://perldoc.perl.org/Getopt/Long.html Getopt::Long]		* [http://perldoc.perl.org/Getopt/Long.html Getopt::Long]
	* File::Find		* File::Find
			* [http://bonsai.hgc.jp/~mdehoon/software/cluster/cluster.pdf Algorithm::Cluster]

	= Variables =		= Variables =

2010-11-18T19:20:43Z

Search directories

← Older revision		Revision as of 19:20, 18 November 2010
Line 90:		Line 90:

	= Search directories =		= Search directories =
	* -~~Idir : same as "~~use lib dir_name"		perl -Idir_name file.pl
			<=>
			cat file.pl
			use lib dir_name ;

	default: /usr/include & /usr/lib/perl		default: /usr/include & /usr/lib/perl
	add dirs to PERLLIB env variable <=> @INC		add dirs to PERLLIB env variable <=> @INC

2009-09-21T14:35:39Z

Debug

← Older revision		Revision as of 14:35, 21 September 2009
Line 108:		Line 108:
	* '''caller function : shows the context'''		* '''caller function : shows the context'''
	print STDERR "DEBUG: context: ",(caller(0))[3],"\n";		print STDERR "DEBUG: context: ",(caller(0))[3],"\n";

			sub myDie { print STDERR "DEBUG: context: ",(caller(1))[3],"\n"; }
			sub b { myDie(); }

	* Example		* Example

2009-09-21T14:29:06Z

Serialization

← Older revision		Revision as of 14:29, 21 September 2009
Line 143:		Line 143:

	print Data::Dumper->Dump([$result],['result']);		print Data::Dumper->Dump([$result],['result']);

			= Redefine commands =
			* Example:
			use subs 'cmp';

	= Libraries =		= Libraries =

2009-09-18T17:27:06Z

@@ Line 114: / Line 114: @@
    Dumper(\@list);
    Dumper(\%hash);
 = Serialization =
@@ Line 135: / Line 143: @@
    print Data::Dumper->Dump([$result],['result']);
 = Libraries =

2009-09-18T17:26:05Z

@@ Line 1: / Line 1: @@
 = Links =
 * [http://perldoc.perl.org/]
 * [http://perltraining.com.au/notes/sysadmin.pdf SysAdmin Perl]
@@ Line 13: / Line 14: @@
 = POD =
 * [http://en.wikipedia.org/wiki/Plain_Old_Documentation POD]; pod2html  pod2latex pod2man   pod2text  pod2usage
 * make sure to leave 1 empty line before/after cut
@@ Line 25: / Line 27: @@
    =cut
    sub max
+   {
@@ Line 61: / Line 50: @@
    sub max(number,number) Returns max of 2 numbers
    sub min(number,number) Returns min of 2 numbers
 = In place editing =
 * Edit a file in place: -i
    perl -i.bck script.pl xxx
@@ Line 108: / Line 108: @@
 * '''caller function : shows the context'''
    print STDERR "DEBUG: context: ",(caller(0))[3],"\n";
    use Data::Dumper;
    ...
    Dumper(\@list);
    Dumper(\%hash);
 = Libraries =

2009-09-18T13:22:59Z

Map

← Older revision		Revision as of 13:22, 18 September 2009
Line 27:		Line 27:
	= Map =		= Map =

	sub addString		sub addString
	{		{
	return @_[0].$_[1];		return @_[0].$_[1];
	}		}
	~~###################~~

	@myNames = ('jacob', 'alexander', 'ethan', 'andrew');		@myNames = ('jacob', 'alexander', 'ethan', 'andrew');
	@ucNames = map(addString($_,"."), @myNames);		@ucNames = map(addString($_,"."), @myNames);

			@a = (1,3,5);
	@a = (1,3,5);
	@b = (2,4,6);		@b = (2,4,6);
	@merged_list = merge(@a,@b); # (1,2,3,4,5,6)		@merged_list = merge(@a,@b); # (1,2,3,4,5,6)

2009-09-17T20:36:58Z

@@ Line 25: / Line 25: @@
    =cut
    sub max
+   {