comment on

This uses the same principle as ++GrandFather described. See Notes below for differences and other features.

#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

my ($in1, $in2, $out) = qw{tmp01 tmp02 tmp11_quick};
my (%data, @headings);

{
    open my $fh, '<', $in1;

    while (<$fh>) {
        if ($. == 1) {
            push @headings, split;
        }
        else {
            my ($pep, $prot) = split;
            push @{$data{$pep}}, $prot;
        }
    }
}

{
    my $fmt = "%-9s %-9s %-10s %-8s\n";
    open my $fh_in, '<', $in2;
    open my $fh_out, '>', $out;

    while (<$fh_in>) {
        my ($id, @rest) = split;

        if ($. == 1) {
            printf $fh_out $fmt, @headings, @rest;
        }
        else {
            for (@{$data{$id}}) {
                printf $fh_out $fmt, $id, $_, @rest;
            }
        }
    }
}
[download]

Output:

PeptideID ProteinID SpectrumID Sequence
6         109521    53663      KMGEGR
7         741       53663      KPPSGK
11        681       144492     NNDALR
11        780       144492     NNDALR
20        2352      15547      SPAKPK
27        1490      55547      LHKPPK
27        1491      55547      LHKPPK
27        1492      55547      LHKPPK
28        51996     55547      LFVGRK
29        1490      55504      LHKPPK
29        1491      55504      LHKPPK
29        1492      55504      LHKPPK
30        1490      55602      LHKPPK
30        1491      55602      LHKPPK
30        1492      55602      LHKPPK
[download]

Notes:

This code deals with real files, not in-memory files.
All I/O is performed in anonymous blocks. Files are only open while needed. Filehandles close automatically at the end of these blocks.
autodie removes the need to hand-craft your own I/O exception messages. It also won't make mistakes like you have in a later post: file with I/O problem is tmp01_quick; message refers to a different file, i.e. donor_82_01.csv. (You have three errors like that.)
When I copied your data to files on my system, the tabs became spaces. I only needed split without arguments; you should continue to use split /\t+/. You should also take note of chomp used in GrandFather's code.
I've used printf to improve output formatting; however, that may not be what you want.

You should also take a look at Text::CSV. (Note, it runs faster if you also have Text::CSV_XS installed.)

— Ken

In reply to Re: match two files by kcott
in thread match two files by yueli711

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