Parsing in perl?

perllearner007 has asked for the wisdom of the Perl Monks concerning the following question:

Replies are listed 'Best First'.
Re: Parsing in perl? by Anonymous Monk on Dec 08, 2011 at 05:01 UTC
perlintro, perlrun, B::Deparse, ... parse tab ... bioperl ... Editing just one column in a file `$ cat junk BRCA1:breast cancer 1, early onset TNF: tumor necrosis factor OMG:oligodendrocyte myelin glycoprotein $ perl -F: -lane " print $F[0]; " junk BRCA1 TNF OMG $ perl -MO=Deparse -F: -lane " print $F[0]; " junk BEGIN { $/ = "\n"; $\ = "\n"; } LINE: while (defined($_ = <ARGV>)) { chomp $_; our(@F) = split(/:/, $_, 0); print $F[0]; } -e syntax OK` [download]	[reply] [d/l]
Re: Parsing in perl? by ansh batra (Friar) on Dec 08, 2011 at 05:08 UTC
#! usr/bin/perl -w open(FILE,"<gene.txt"); my @lines=<FILE>; close(FILE); foreach my $line(@lines) { if($line=~/:/) { print "$`\n"; } } [download] output `BRCA1 TNF OMG` [download] PS: $` is a special variable used to extract data before the regular expression	[reply] [d/l] [select]
Re^2: Parsing in perl? by Anonymous Monk on Dec 08, 2011 at 05:23 UTC
Or without the $` ( `$PREMATCH` ) imposed penalty ( see, depending on your shell, perldoc -v "$`" or perldoc -v '$`') , its more Modern Perl-ish `#!usr/bin/perl -- use strict; use warnings; use autodie qw/ open close /; # error checking open my($file), '<', 'gene.txt'; while( <$file> ){ print $1 if /^([^:]+):/; } close $file;` [download]	[reply] [d/l] [select]
Re: Parsing in perl? by CountZero (Bishop) on Dec 08, 2011 at 22:48 UTC
So many ways to do it! `use Modern::Perl; say +(split ':')[0] while (<DATA>); __DATA__ BRCA1:breast cancer 1, early onset TNF: tumor necrosis factor OMG:oligodendrocyte myelin glycoprotein` [download] CountZero A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James	[reply] [d/l]
Re: Parsing in perl? by TJPride (Pilgrim) on Dec 08, 2011 at 13:27 UTC
`use strict; use warnings; my @list; open (FH, 'sample.txt') \|\| die; while (<FH>) { push @list, $1 if m/^(.+?):/; } print "@list";` [download]	[reply] [d/l]
Re: Parsing in perl? by planetscape (Chancellor) on Dec 08, 2011 at 15:38 UTC
See also: Perl and Bioinformatics HTH, planetscape	[reply]
Re: Parsing in perl? by Anonymous Monk on Dec 08, 2011 at 23:44 UTC
Thank you all for your replies.	[reply]