in reply to Print the data following few specific lines in perl

You can use select to choose between your 2 output files: 
use strict;
use warnings;

my $in = $ARGV[0];
my $p  = $ARGV[1];
my $s  = $ARGV[2];

open IN   , "<$in" or die $!;
open P_OUT, ">$p" or die $!; 
open S_OUT, ">$s" or die $!;

while (<IN>) {
    if (/^>/) {
        if (/pair:/) {
            select P_OUT;
        }
        else{
            select S_OUT;
        }
    }
    print;
}

close(IN);
close(P_OUT);
close(S_OUT);

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Re^2: Print the data following few specific lines in perl
by ad23 (Acolyte) on Jul 01, 2010 at 18:30 UTC

    Thanks for your help.

    But all the above codes are printing just the header lines. I still am not able to print the data after the header lines for each record.

    Am I am not seeing the obvious???

[reply]
      It seems to work for me.

      Download my code and save it as a file named 847578.pl. Then download your data and save it in a file named fasta.txt. Then execute this at your command line: 

      perl ./847578.pl fasta.txt p.txt s.txt

      [download]

      I get 2 output files. This is the contents of file p.txt: 

      >CVSF10000.x1 bg|356789 pair:789860
ATGCGTAGCTGATGTGCTGCTGATGCTAGTCGTCGTAGCTGATGCATGCTGATCGTAGTGCTCGATGCTA
GTCGTAGTCGTAGTCGTAGCGACTGATGCGATCGTAGTCGGATGATGCTGACTGATGCTGATCTGTACGT
CGTAGCTGATGCATGCGCTAGTAGCT
>CVSF10000.y1 bg|356790 pair:789859
GCTAGTCGATGCTGATGCTGTAGCTAGCGTAGTCGTACGCGCGCGCGCGCGTTTTTTGTGACGTCGTAGT
CCGTAGCTGATGCGATGCTAGTGCTGTGTCAGCTGATGTCGTGTGTAGCTGATGCTGATCGTTCGTGTGT
CGATGCTGATGCTAGTCGTAGTGTAT
>CVSF10001.x1 bg|356791 pair:789862
AGTCGTAGTCGTAGCTGTAGCTGATGCTGTGTACGATGCTGATGCGATGCGTAGCGTAGCATCGATGCTA
CGACTAGTCGTAGTCGTC
>CVSF10001.y1 bg|356792 pair:789861
CGTAGCTGATGCTGATCGTAGTCGTAGTCGATGCGATGCTAGTCGTAGCTGTAGCTGATGCTGCGTGCTG
CAGTCGATGCTAGTCGATGCTGATCGTCTAGCAT

      [download]

      This is the contents of file s.txt: 

      >CVSF43565.d1 bg|346278
CAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATGTATGGCAGACAACTGTTCTGGGAGTTGG
ATCCGGGTAAGCAACGGGTCCACATATCTCCACAATCTCATAAGGGGCCAACATAGCGGGGGAGCTAACT
TGCCTTTGATTCCAAACCGTTGCACTCCTTTGGTCGGGGAAACTCGAAGGTACACATGATCACCAAGGTC
GAACTGCAGGGGTCTTCTCCGCTGGTCGGAGTAGCTCTTCTGTCAAGATTGGGCGGCCTTGAGATGTGCT
TGAATTACCTTCACTTGCTCTTCGGCTTCTGCCACTTAAGTCAGGGCCATAGACCTGTCTCTCCCCTGGG
CAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATGTATGGCAGACAACTGTTCTGGGAGTTGG
ATCCGGGTAAGC
>CVSF43566.d1 bg|346279
CAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATGTATGGCAGACAACTGTTCTGGGAGTTGG
ATCCGGGTAAGCCAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATGTATGGCAGACAACTGT
TCTGGGAGTTGGAATGCTAGTCGATCGCCAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATG
TTGGCAGACAACTGTTCTGGGAGTTGGATCCGGGTAAGCCAGACACACTTCTTTTAGTTGAGACACATGG
AAAACATCATGTATGGCAGACAACTGTTCTGGGAGTTGGATCCGGGTAAGC
>CVSF43567.d1 bg|346280
CGTAGCTGATGCTGTGCTGTTGTGTCGGGGGGATATATATATATATATGGGGTCGTAGTCGTAGCGCTAG
TATGCTAGCAGCGTAGATGCTGATCGATGCTGATGCTGATCGTAGTCGTAGGCTAGTGCGATCGTAGTCG
TAGTCGATGCTGATGCGTAGCTGATGTGCTGCTGATGCTAGTCGTCGTAGCTGATGCATGCTGATCGTAG
TGCTCGATGCTAGTCGTAGTCGTAGTCGTAGCGACTGATGCGATCGTAGTCGGATGCTAGCACGTAGCTG
GCTCGATGCTGATGCTGAT

      [download]
[reply]
[d/l]
[select]

        It works now after I copied your code and renamed my files.

        Thanks!!!!

[reply]

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