bin/add_seq2sims

#!/usr/bin/env perl

use strict;
use warnings;

use Data::Dumper;
use Getopt::Long;

my $verbose  = 0;
my $in_sim   = '';
my $seq_file = '';
my $out_sim  = '';
my $usage    = qq($0
Input:  1. m8 format blast / blat file
        2. tabbed file with id \t seq
Output: inputed sims file with sequence for each query appened to each line
NOTE: inputed sim and tab file must be sorted by query / id

m8: query, subject, identity, length, mismatch, gaps, q_start, q_end, s_start, s_end, evalue, bit_score

  --in_sim    file name   Required. Name of input sim file. Sorted by query id.
  --seq_file  file name   Required. Name of tabbed id/seq file. Sorted by id.
  --out_sim   file name   Required. Name of appended output sim file.
  --verbose               Optional. Verbose output.

);

if ( (@ARGV > 0) && ($ARGV[0] =~ /-h/) ) {
    print STDERR $usage; exit 1;
}
if ( ! GetOptions(
        "verbose!"   => \$verbose,
        "in_sim=s"   => \$in_sim,
        "seq_file=s" => \$seq_file,
        "out_sim=s"  => \$out_sim
    ) ) {
    print STDERR $usage; exit 1;
}
unless ($in_sim && $seq_file && $out_sim && (-s $in_sim) && (-s $seq_file)) {
    print STDERR $usage . "Missing file input.\n"; exit 1;
}

print STDOUT "Reading file $in_sim ... " if ($verbose);
open(SIM, "<$in_sim")   || die "Can't open file $in_sim!\n";
open(SEQ, "<$seq_file") || die "Can't open file $seq_file!\n";
open(OUT, ">$out_sim")  || die "Can't open file $out_sim!\n";

my $s_num = 0;
my $q_num = 0;
my $prev  = "";
my $seql  = <SEQ>;
chomp $seql;
my ($id, $seq) = split(/\t/, $seql);

while (my $siml = <SIM>) {
    chomp $siml;
    if ($siml =~ /^(.+?)\t(.+)$/) {
        $s_num += 1;
        my $query = $1;
        my $rest  = $2;
        unless ($query) { next; }
        if ($prev ne $query) {
            while ($id ne $query) {
                $seql = <SEQ>;
                unless (defined($seql)) { last; }
                chomp $seql;
                ($id, $seq) = split(/\t/, $seql);
            }
            $q_num += 1;
            print OUT "$query\t$rest\t$seq\n";
        } else {
            print OUT "$query\t$rest\t$seq\n";
        }
        $prev = $query;
    }
}
close OUT;
close SEQ;
close SIM;

print STDOUT "Done: $q_num sequences added to $s_num sims\n" if ($verbose);
exit 0;