Re: First header missing from FASTA data

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]

Comment on Re: First header missing from FASTA data Select or Download Code

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Re^2: First header missing from FASTA data by Anonymous Monk on Mar 15, 2012 at 03:51 UTC
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`?	[reply] [d/l] [select]

Replies are listed 'Best First'.

Re^2: First header missing from FASTA data
by Anonymous Monk on Mar 15, 2012 at 03:51 UTC

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?

[reply]
[d/l]
[select]