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#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib "$FindBin::RealBin/../../PerlLib";
use Pipeliner;
use File::Basename;
my $usage = <<__EOUSAGE__;
#######################################################################################
#
# --outfmt6_grouped <string> outfmt6 grouped output
#
# --min_pct_len <int> minimum percent length covered by pairwise matches
#
# --min_per_id <int> minimum percent identity
#
# --inflation_factor <float> inflation factor for MCL clustering
#
#######################################################################################
__EOUSAGE__
;
my $help_flag;
my $outfmt6_grouped_file;
my $inflation_factor;
my $min_pct_len;
my $min_per_id;
&GetOptions ( 'h' => \$help_flag,
'outfmt6_grouped=s' => \$outfmt6_grouped_file,
'min_pct_len=i' => \$min_pct_len,
'min_per_id=i' => \$min_per_id,
'inflation_factor=f' => \$inflation_factor,
);
if ($help_flag) {
die $usage;
}
if (@ARGV) {
die "Error, dont understand parameters @ARGV";
}
unless ($outfmt6_grouped_file && $inflation_factor && $min_pct_len && $min_per_id) {
die $usage;
}
# add MCL to PATH setting
$ENV{PATH} = "/seq/regev_genome_portal/SOFTWARE/MCL/bin/:$ENV{PATH}";
main: {
my $filtered_hits = basename($outfmt6_grouped_file . ".minLEN_${min_pct_len}_pct_len.minPID_${min_per_id}.abc");
my $checkpoint = ".$filtered_hits.ok";
if (! -e $checkpoint) {
my %best_hits;
open (my $fh, $outfmt6_grouped_file) or die "Error, cannot open file $outfmt6_grouped_file";
while (<$fh>) {
if (/^\#/) { next; }
chomp;
my @x = split(/\t/);
my ($transA, $transB, $per_id, $E_value, @rest) = split(/\t/);
my $per_len_match = pop @rest;
if ($per_len_match >= $min_pct_len && $per_id >= $min_per_id) {
my $geneA = &parse_gene_name($transA);
my $geneB = &parse_gene_name($transB);
if ($geneA eq $geneB) { next; }
($geneA, $geneB) = sort ($geneA, $geneB);
my $gene_pair_token = join("$;", $geneA, $geneB);
my $lowest_evalue = $best_hits{$gene_pair_token};
if ( (! defined $lowest_evalue) || $lowest_evalue > $E_value) {
$best_hits{$gene_pair_token} = $E_value;
}
}
}
# write best hits file
open (my $ofh, ">$filtered_hits") or die "Error, cannot write to $filtered_hits";
foreach my $gene_pair_token (keys %best_hits) {
my ($geneA, $geneB) = split(/$;/, $gene_pair_token);
my $E_value = $best_hits{$gene_pair_token};
print $ofh join("\t", $geneA, $geneB, $E_value) . "\n";
}
close $ofh;
`touch $checkpoint`;
}
my $pipeliner = new Pipeliner(-verbose => 1);
my $cmd = "mcxload -abc $filtered_hits --stream-mirror --stream-neg-log10 "
. " -stream-tf 'ceil(200)' -o $filtered_hits.mci -write-tab $filtered_hits.tab";
$pipeliner->add_commands( new Command($cmd, ".$filtered_hits.tab.ok") );
$inflation_factor = sprintf("%.1f", $inflation_factor);
my $inflation_factor_dec_removed = $inflation_factor;
$inflation_factor_dec_removed =~ s/\.//;
$cmd = "mcl $filtered_hits.mci -I $inflation_factor";
my $mcl_outfile = "out.$filtered_hits.mci.I$inflation_factor_dec_removed";
$pipeliner->add_commands( new Command($cmd, ".$mcl_outfile.ok"));
$cmd = "mcxdump -icl $mcl_outfile -tabr $filtered_hits.tab -o dump.$mcl_outfile";
$pipeliner->add_commands( new Command($cmd, ".dump.$mcl_outfile.ok"));
$pipeliner->run();
exit(0);
}
####
sub parse_gene_name {
my ($trans_info) = @_;
my ($gene_symbol, $trans_id);
if (/;/) {
($trans_id, $gene_symbol) = split(/;/, $trans_info);
}
elsif (/\|/) {
($gene_symbol, $trans_id) = split(/\|/, $trans_info);
}
if ($gene_symbol) {
return($gene_symbol);
}
else {
return($trans_info);
}
}
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