Hello All,

I am trying to parse a fasta file using perl. The following is the input file: 

>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
>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]

I want to write the lines(and the data that follows) with "pairs" field in one file and the lines without "pairs" field in another.

However, with the following code I am only able to write the header lines. But I also want the data following the header line(ATGCTAGCTG....) to be included in the output files.

Any inputs?? 

#!/usr/bin/perl

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>){
    chomp;
    
    if(/^>/){
    my @header = split / /;
    
    if($header[2] ne ''){
        print P_OUT "$header[0]"." "."$header[1]"." "."$header[2]\n";
    }
    else{
        print S_OUT "$header[0]"." "."$header[1]\n";
    }
    }
    #unless(/^>/){
    #print OUT "$_\n";
    #next;
    #}
}

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

[download]

Thanks!!!

In reply to Print the data following few specific lines in perl by ad23

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