/
blastm8_filter.pl
executable file
·213 lines (197 loc) · 7.52 KB
/
blastm8_filter.pl
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#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case);
my ($blastfile,$dbfile, $queryfile, $excludefile) = ("","","","");
my ($evalue, $perc_identity, $length, $bitscore, $max_target_seqs, $hsp_per_target, $qregex, $dregex) = ("","","","","","","","");
my ($qcov, $dcov, $combinehsp) = ("","","");
GetOptions (
"db:s" => \$dbfile,
"query:s" => \$queryfile,
"blastfile:s" => \$blastfile,
"excludefile:s" => \$excludefile,
"perc_identity:f" => \$perc_identity,
"evalue:f" => \$evalue,
"length:i" => \$length,
"score:f" => \$bitscore,
"max_target_seqs:i" => \$max_target_seqs,
"hsp_per_target:i" => \$hsp_per_target,
"qcov:s" => \$qcov,
"dcov:s" => \$dcov,
"qregex:s" => \$qregex,
"dregex:s" => \$dregex,
"combinehsp" => \$combinehsp,
);
my ($current_target_seqs, $current_hsps, $qid, $did) = (0,0,"","");
if (!$blastfile or ($qcov and not $queryfile) or ($dcov and not $dbfile) or ($combinehsp and not $dcov and not $qcov)
or ($combinehsp and $hsp_per_target))
{
die <<USAGE;
Usage:
blastm8_filter.pl
-b, --blastfile : <tabular/m8/outfmt6 blast output> MANDATORY, all others optional
-ex,--excludefile:<tabular file with col1=contig, col2=st, col3=en. If any blast hit
overlaps these intervals, it will be excluded
-e, --evalue : evalue cutoff eg. -e 1e-5 filters hits <= 1e-5
-l, --length : length cutoff eg. -l 100 filters hits with alignment length >= 100
-s, --bitscore : bitscore cutoff (-s 200 filters hits with bitscore >= 100
-q, --qregex : regexp to filter only some query sequences,
eg -q "^clc" only picks queries beginning with clc
-d, --dregex : regexp to filter only some database/target/ref sequences,
eg -d "_c|_s" only picks those database sequences that match _c or _s
-m, --max_target_seqs : assuming blast file is sorted as output by blast/blast+,
-m 1 will pick only 1 target seq per query
-h, --hsp_per_target : assuming blast file is sorted as output by blast/blast+,
-h 1 will pick only 1 hsp per query_target pair.
Using with -m 1 guarantees only one hsp per query
--qcov : proportion of query covered by hit (0.0-1.0). Must specify query fasta file
--query : query fasta file
--dcov : proportion of database covered by hit (0.0-1.0). Must specify db fasta file
--db : db fasta file
-c, --combinehsp: Use this ONLY if you want to combine all hsps for a hit when calculating qcov/dcov. Doesn't make sense
to use this with -h 1
USAGE
}
my %exclude_hash;
if (-r $excludefile)
{
my $exclude_fh = &read_fh($excludefile);
while (<$exclude_fh>)
{
next unless /^>?(\S+?)[\t_ ](\d+)[\t_ ](\d+)$/;
push @{$exclude_hash{$1}}, [$2,$3];
}
for my $chrontig (keys %exclude_hash)
{
@{$exclude_hash{$chrontig}} = sort { $a->[0] <=> $b->[0] } @{$exclude_hash{$chrontig}};
}
}
my $qsequences = &fastafile2hash($queryfile) if $queryfile;
my $dsequences = &fastafile2hash($dbfile) if $dbfile;
my ($current_hit_q_string, $current_hit_d_string, $current_hit_toprint) = ("","","");
my $blastfh = &read_fh($blastfile);
while (my $line = <$blastfh>)
{
next if $line =~ /^#/ or $line =~ /^\s*$/;
my @blastm8 = split(/\t/, $line);
die "Input not in blast -m 8 or blast+ -outfmt 6 tabular format\n" if scalar @blastm8 < 12;
next if $evalue and eval($blastm8[10]) > $evalue;
next if $length and $blastm8[3] < $length;
next if $perc_identity and $blastm8[2] < $perc_identity;
next if $bitscore and $blastm8[11] < $bitscore;
next if $qregex and $blastm8[0] !~ /$qregex/;
next if $dregex and $blastm8[1] !~ /$dregex/;
my ($qst, $qen, $dst, $den) = ($blastm8[6],$blastm8[7],$blastm8[8],$blastm8[9]);
($qst,$qen) = ($qen,$qst) if $qst > $qen;
($dst,$den) = ($den,$dst) if $dst > $den;
my $qlen = $qen - $qst + 1;
my $dlen = $den - $dst + 1;
if ($blastm8[0] =~ /^(.+?)_(\d+)_(\d+)$/) { $qst = $qst + $2 - 1; $qen = $qen + $2 - 1; $blastm8[0] = $1 }
if ($blastm8[1] =~ /^(.+?)_(\d+)_(\d+)$/) { $dst = $dst + $2 - 1; $den = $den + $2 - 1; $blastm8[1] = $1 }
next if exists $exclude_hash{$blastm8[0]} and &binary_search_intervals ( $exclude_hash{$blastm8[0]}, $qst, $qen );
next if exists $exclude_hash{$blastm8[1]} and &binary_search_intervals ( $exclude_hash{$blastm8[1]}, $dst, $den );
next if $qcov and not defined $$qsequences{$blastm8[0]};
next if $dcov and not defined $$dsequences{$blastm8[1]};
if (not $combinehsp)
{
next if $qcov and $qlen/length($$qsequences{$blastm8[0]}{seq}) < $qcov;
next if $dcov and $dlen/length($$dsequences{$blastm8[1]}{seq}) < $dcov;
}
if ($qid ne $blastm8[0])
{
$current_target_seqs = 1;
}
if (($qid eq $blastm8[0] or $qid eq "") and $did ne $blastm8[1])
{
$current_target_seqs++;
}
if("$qid$did" ne "$blastm8[0]$blastm8[1]")
{
# new hit
$current_hsps = 1;
# check if old hsp needs to be printed if $combinehsp is on
if ($combinehsp and "$qid$did")
{
print $current_hit_toprint unless
$qcov and ($current_hit_q_string=~tr/1/1/)/length($$qsequences{$qid}{seq}) <$qcov or
$dcov and ($current_hit_d_string=~tr/1/1/)/length($$dsequences{$did}{seq}) <$dcov;
}
$current_hit_toprint = $line;
$current_hit_q_string = "0" x length($$qsequences{$blastm8[0]}{seq}) if $queryfile;
$current_hit_d_string = "0" x length($$dsequences{$blastm8[1]}{seq}) if $dbfile;
} else
{
$current_hsps++
}
$qid = $blastm8[0];
$did = $blastm8[1];
next if $max_target_seqs and $current_target_seqs > $max_target_seqs;
next if $hsp_per_target and $current_hsps > $hsp_per_target;
if ($combinehsp)
{
substr($current_hit_q_string, $qst -1, $qlen, "1" x $qlen) if $queryfile;
substr($current_hit_d_string, $dst -1, $dlen, "1" x $dlen) if $dbfile;
$current_hit_toprint .= $line if $current_hsps >1;
} else
{
print $line;
}
}
###################################################################################################
sub fastafile2hash
{
my $fastafile = shift @_;
my $changecase = "N"; $changecase = shift @_ if @_;
my %sequences;
my $seqid = "";
my $fh = &read_fh($fastafile);
while (<$fh>)
{
if (/^>(\S+)(.*)/) {
$seqid = $1;
$sequences{$seqid}{desc} = $2;
}
elsif ($changecase eq "L") { chomp($sequences{$seqid}{seq} .= lc($_)) }
elsif ($changecase eq "U") { chomp($sequences{$seqid}{seq} .= uc($_)) }
elsif ($changecase eq "N") { chomp($sequences{$seqid}{seq} .= $_) }
}
close $fh;
return \%sequences;
}
###################################################################################################
sub read_fh {
my $filename = shift @_;
my $filehandle;
if ($filename =~ /gz$/) {
open $filehandle, "gunzip -dc $filename |" or die $!;
}
else {
open $filehandle, "<$filename" or die $!;
}
return $filehandle;
}
###################################################################################################
sub binary_search_intervals
{
my ($array_ref, $range_st, $range_en) = @_;
my @sorted = @$array_ref;
my $low_index = 0; my $high_index = $#sorted;
my $found = 0;
while ( $low_index <= $high_index and not $found )
{
my $mid_index = int ( ( $low_index + $high_index ) / 2 );
if ( $sorted[$mid_index]->[0] <= $range_en and $sorted[$mid_index]->[1] >= $range_st )
{
$found = 1;
return $mid_index + 1;
}
if ( $sorted[$mid_index]->[0] < $range_en )
{
$low_index = $mid_index + 1;
} else
{
$high_index = $mid_index - 1;
}
}
return $found;
}