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#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $help_flag;
my $usage = <<__EOUSAGE__;
#################################################################################################
#
# Required:
#
# --details <string> compreh_init_build.details filename
# --blast <string> blast.outfmt6.w_pct_hit_length filename
#
# Optional:
#
# --min_pct_hit_len <float> min length of alignment coverage of hit (default: 80)
# --pasa_validations <string> incorporate notes from pasa's alignment validations file (alignment.validations.out)
#
#################################################################################################
__EOUSAGE__
;
my $compreh_details_file;
my $blast_file;
my $min_pct_hit_len = 80;
my $pasa_validations_file;
&GetOptions ( 'h' => \$help_flag,
'details=s' => \$compreh_details_file,
'blast=s' => \$blast_file,
'min_pct_hit_len=f' => \$min_pct_hit_len,
'pasa_validations=s' => \$pasa_validations_file,
);
if ($help_flag) {
die $usage;
}
unless ($compreh_details_file && $blast_file) {
die $usage;
}
my %pasa_validations_info;
if ($pasa_validations_file) {
open (my $fh, $pasa_validations_file) or die $!;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $acc = $x[1];
my $note = $x[14];
if ($note) {
$pasa_validations_info{$acc} .= $note . "; ";
}
}
close $fh;
}
my %FL_mappings;
{
open (my $fh, $blast_file) or die $!;
while (<$fh>) {
if (/^\#/) { next; }
chomp;
my @x = split(/\t/);
my $pct_hit_len = $x[13];
if ($pct_hit_len < $min_pct_hit_len) {
next;
}
my $query = $x[0];
my $hit = $x[1];
my $annot = $x[14];
my $Evalue = $x[10];
$FL_mappings{$query} = join("\t", $hit, $annot, $Evalue, $pct_hit_len);
}
close $fh;
}
my $prev_gene = "";
open (my $fh, $compreh_details_file) or die $!;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $gene = $x[0];
my $acc = $x[1];
if (my $mappings = $FL_mappings{$acc}) {
$mappings =~ s/\t/ /g;
push (@x, $mappings);
}
else {
push (@x, "");
}
if (my $validation_note = $pasa_validations_info{$acc}) {
push (@x, "validation_note: $validation_note");
}
if ($gene ne $prev_gene) {
print "\n";
}
$prev_gene = $gene;
print join("\t", @x) . "\n";
}
exit(0);
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