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

Hi Everyone,

I am doing a regex on my FASTA data which contains multiple protein sequences and their description as a header line. My output should consist of a header line and the sequence. When i print it to FILE my first header is missing. all other header lines are present. Any insight would be very welcome. below is my perl script: 

use strict; 
use warnings;
 
open IN, "zea_mays.txt";
open OUT, ">zea_mays1.txt";
my @peptides; 
my $seq;
my $flag = 0;
while(my $line = <IN>){
    chomp($line);  #check the chomp function
    if ($line =~ /^>/) {
        if ($flag == 0){ #the first protein entry, which means nothing
+ in the memory to do
            $flag = 1;
            next; 
        }
        print "\n";
        print OUT " $line\n ";
    }else {
        $line =~ s/\s//g;
        my @peptides  = split(/(?<=[RK](?!P))/,$line);
        print OUT "@peptides\n";
        
    }
}
close IN;
close OUT;

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Replies are listed 'Best First'.
Re: First header missing from FASTA data
by tangent (Parson) on Mar 15, 2012 at 01:42 UTC
    When you say if ($flag == 0) { ... next;} you are telling the program not to print the first header line. Remove that if block and it will. NYULMC?
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Re: First header missing from FASTA data
by Khen1950fx (Canon) on Mar 15, 2012 at 03:13 UTC
    I edited your script and used <code></code> tags---never leave home without them:). 
    #!/usr/bin/perl -l

use strict;
use warnings;

my(@lines) = '/tmp/zea_mays.txt';
my $log   = '/tmp/zea_mays.log';

die $! unless open IN,  '<', @lines;
die $! unless open OUT, '>', $log;

my $peptides;
my $seq;
my $flag = 0;
while ( defined( my $line = readline \*IN ) ) {
    do {
        foreach $line (@lines) {
            chomp $line;
            if ( $line =~ /^>/ ) {
                next if $flag > 0;
                print "\n";
                print OUT "$line";
            }
            else {
                $line =~ s/\s//g;
                my (@peptides) = split( /(?<=RK(?!P))/, $line );
                print OUT "@peptides";
            }
        }
    };
}
close IN;
close OUT;

    [download]
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[select]

      Not a very good translation of: 

      use strict;
use warnings;

open IN, "zea_mays.txt";
open OUT, ">zea_mays1.txt";
my @peptides;
my $seq;
my $flag = 0;
while(my $line = <IN>){
    chomp($line);  #check the chomp function
    if ($line =~ /^>/) {
        if ($flag == 0){ #the first protein entry, which means       n
+othing in the memory to do
            $flag = 1;
            next;
        }
        print "\n";
        print OUT " $line\n ";
    }else {
        $line =~ s/\s//g;
        my @peptides  = split(/(?<=[RK](?!P))/,$line);
        print OUT "@peptides\n";

    }
}
close IN;
close OUT;

      [download]


      my(@lines) = '/tmp/zea_mays.txt';

      [download]

      Why store a scalar value in an array? 

      while ( defined( my $line = readline \*IN ) ) {
    do {
        foreach $line (@lines) {

      [download]

      And then here you loop through that single value, a file name, and ignore the lines read from the file.    And what's up with the superfluous do block? 



                      my (@peptides) = split( /(?<=RK(?!P))/, $line );

      [download]

      The original used the character class [RK] but you are using the string RK?

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Re: First header missing from FASTA data
by bugiep (Initiate) on Mar 15, 2012 at 12:10 UTC
    Very many thanks guys i appreciate your assistance. i solved the problem as suggested by 'tangent'. Khen1950fx i shall study the way you go about the problem it might come in handy sometime.
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