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infernal-tblout2gff.pl
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#!/usr/bin/env perl
# infernal-tblout2gff.pl: convert cmsearch or cmscan tblout files to GFF format
# an important point of above ref:
# "Start is always less than or equal to end"
# EPN, Fri Jun 7 11:07:38 2019
#
#
use strict;
use warnings;
use Getopt::Long;
my $in_tblout = ""; # name of input tblout file
my $usage;
$usage = "infernal-tblout2gff.pl\n\n";
$usage .= "Usage:\n\n";
$usage .= "infernal-tblout2gff.pl [OPTIONS] <cmsearch tblout file>\n\tOR\n";
$usage .= "infernal-tblout2gff.pl --cmscan [OPTIONS] <cmscan tblout file>\n\tOR\n";
$usage .= "infernal-tblout2gff.pl --cmscan --fmt2 [OPTIONS] <cmscan --fmt 2 tblout file>\n\n";
$usage .= "\tOPTIONS:\n";
$usage .= "\t\t-T <n> : minimum bit score to include is <n>\n";
$usage .= "\t\t-E <x> : maximum E-value to include is <x>\n";
$usage .= "\t\t--cmscan : tblout file was created by cmscan\n";
$usage .= "\t\t--source <s> : specify 'source' field should be <s> (e.g. tRNAscan-SE)\n";
$usage .= "\t\t--fmt2 : tblout file was created with cmscan --fmt 2 option\n";
$usage .= "\t\t--all : output all info in 'attributes' column [default: E-value]\n";
$usage .= "\t\t--none : output no info in 'attributes' column [default: E-value]\n";
$usage .= "\t\t--desc : output desc field in 'attributes' column [default: E-value]\n";
$usage .= "\t\t--version <s>: append \"-<s>\" to 'source' column\n";
$usage .= "\t\t--extra <s> : append \"<s>;\" to 'attributes' column\n";
$usage .= "\t\t--hidedesc : do not includ \"desc\:\" prior to desc value in 'attributes' column\n";
my $do_minscore = 0; # set to '1' if -T used
my $do_maxevalue = 0; # set to '1' if -E used
my $minscore = undef; # defined if if -T used
my $maxevalue = undef; # defined if -E used
my $do_cmscan = 0; # set to '1' if --cmscan used
my $do_fmt2 = 0; # set to '1' if --fmt
my $do_all_attributes = 0; # set to '1' if --all
my $do_no_attributes = 0; # set to '1' if --none
my $do_de_attributes = 0; # set to '1' if --desc
my $version = undef; # defined if --version used
my $extra = undef; # defined if --extra used
my $do_hidedesc = 0; # set to 1 if --hidedesc used
my $opt_source = undef; # set to <s> if --source <s> used
&GetOptions( "T=s" => \$minscore,
"E=s" => \$maxevalue,
"cmscan" => \$do_cmscan,
"source=s" => \$opt_source,
"fmt2" => \$do_fmt2,
"all" => \$do_all_attributes,
"none" => \$do_no_attributes,
"desc" => \$do_de_attributes,
"version=s" => \$version,
"extra=s" => \$extra,
"hidedesc" => \$do_hidedesc);
if(scalar(@ARGV) != 1) { die $usage; }
my ($tblout_file) = @ARGV;
if(defined $minscore) { $do_minscore = 1; }
if(defined $maxevalue) { $do_maxevalue = 1; }
if($do_minscore && $do_maxevalue) {
die "ERROR, -T and -E cannot be used in combination. Pick one.";
}
if(($do_all_attributes) && ($do_no_attributes)) {
die "ERROR, --all and --none cannot be used in combination. Pick one.";
}
if(($do_all_attributes) && ($do_de_attributes)) {
die "ERROR, --all and --desc cannot be used in combination. Pick one.";
}
if(($do_no_attributes) && ($do_de_attributes)) {
die "ERROR, --none and --desc cannot be used in combination. Pick one.";
}
if(($do_fmt2) && (! $do_cmscan)) {
die "ERROR, --fmt2 only makes sense in combination with --cmscan";
}
if((defined $opt_source) && (defined $version)) {
die "ERROR, --source and --version are incompatible";
}
if(! -e $tblout_file) { die "ERROR tblout file $tblout_file does not exist"; }
if(! -s $tblout_file) { die "ERROR tblout file $tblout_file is empty"; }
my $source = ($do_cmscan) ? "cmscan" : "cmsearch";
if(defined $version) { $source .= "-" . $version; }
if(defined $opt_source) { $source = $opt_source; }
open(IN, $tblout_file) || die "ERROR unable to open $tblout_file for reading";
my $line;
my $i;
while($line = <IN>) {
if($line !~ m/^\#/) {
chomp $line;
my @el_A = split(/\s+/, $line);
my $nfields = scalar(@el_A);
if((! $do_fmt2) && ($nfields < 18)) {
die "ERROR expected at least 18 space delimited fields in tblout line (fmt 1, default) but got $nfields on line:\n$line\n";
}
if(($do_fmt2) && ($nfields < 27)) {
die "ERROR expected at least 27 space delimited fields in tblout line (fmt 2, --fmt2) but got $nfields on line:\n$line\n";
}
# ref Infernal 1.1.2 user guide, pages 59-61
my $idx = undef;
my $seqname = undef;
my $seqaccn = undef;
my $mdlname = undef;
my $mdlaccn = undef;
my $clan = undef;
my $mdl = undef;
my $mdlfrom = undef;
my $mdlto = undef;
my $seqfrom = undef;
my $seqto = undef;
my $strand = undef;
my $trunc = undef;
my $pass = undef;
my $gc = undef;
my $bias = undef;
my $score = undef;
my $evalue = undef;
my $inc = undef;
my $olp = undef;
my $anyidx = undef;
my $anyfrct1= undef;
my $anyfrct2= undef;
my $winidx = undef;
my $winfrct1= undef;
my $winfrct2= undef;
my $desc = undef;
if($do_fmt2) { # 27 fields
$idx = $el_A[0];
$seqname = ($do_cmscan) ? $el_A[3] : $el_A[1];
$seqaccn = ($do_cmscan) ? $el_A[4] : $el_A[2];
$mdlname = ($do_cmscan) ? $el_A[1] : $el_A[3];
$mdlaccn = ($do_cmscan) ? $el_A[2] : $el_A[4];
$clan = $el_A[5];
$mdl = $el_A[6];
$mdlfrom = $el_A[7];
$mdlto = $el_A[8];
$seqfrom = $el_A[9];
$seqto = $el_A[10];
$strand = $el_A[11];
$trunc = $el_A[12];
$pass = $el_A[13];
$gc = $el_A[14];
$bias = $el_A[15];
$score = $el_A[16];
$evalue = $el_A[17];
$inc = $el_A[18];
$olp = $el_A[19];
$anyidx = $el_A[20];
$anyfrct1= $el_A[21];
$anyfrct2= $el_A[22];
$winidx = $el_A[23];
$winfrct1= $el_A[24];
$winfrct2= $el_A[25];
$desc = $el_A[26];
for($i = 27; $i < $nfields; $i++) { $desc .= "_" . $el_A[$i]; }
}
else { # fmt 1, default
$seqname = ($do_cmscan) ? $el_A[2] : $el_A[0];
$seqaccn = ($do_cmscan) ? $el_A[3] : $el_A[1];
$mdlname = ($do_cmscan) ? $el_A[0] : $el_A[2];
$mdlaccn = ($do_cmscan) ? $el_A[1] : $el_A[3];
$mdl = $el_A[4];
$mdlfrom = $el_A[5];
$mdlto = $el_A[6];
$seqfrom = $el_A[7];
$seqto = $el_A[8];
$strand = $el_A[9];
$trunc = $el_A[10];
$pass = $el_A[11];
$gc = $el_A[12];
$bias = $el_A[13];
$score = $el_A[14];
$evalue = $el_A[15];
$inc = $el_A[16];
$desc = $el_A[17];
for($i = 18; $i < $nfields; $i++) { $desc .= "_" . $el_A[$i]; }
}
# one sanity check, strand should make sense
if(($strand ne "+") && ($strand ne "-")) {
if(($do_fmt2) && (($seqfrom eq "+") || ($seqfrom eq "-"))) {
die "ERROR problem parsing, you specified --fmt2 but tblout file appears to have NOT been created with --fmt 2, retry without --fmt2\nproblematic line:\n$line\n";
}
if((! $do_fmt2) && (($pass eq "+") || ($pass eq "-"))) {
die "ERROR problem parsing, you did not specify --fmt2 but tblout file appears to have been created with --fmt 2, retry with --fmt2\nproblematic line:\n$line\n";
}
die "ERROR unable to parse, problematic line:\n$line\n";
}
if(($do_minscore) && ($score < $minscore)) {
; # skip
}
elsif(($do_maxevalue) && ($evalue > $maxevalue)) {
; # skip
}
else {
my $attributes = "evalue=" . $evalue; # default to just evalue
if($do_all_attributes) {
if($do_fmt2) {
$attributes .= sprintf(";idx=$idx;seqaccn=$seqaccn;mdlaccn=$mdlaccn;clan=$clan;mdl=$mdl;mdlfrom=$mdlfrom;mdlto=$mdlto;trunc=$trunc;pass=$pass;gc=$gc;bias=$bias;inc=$inc;olp=$olp;anyidx=$anyidx;anyfrct1=$anyfrct1;anyfrct2=$anyfrct2;winidx=$winidx;winfrct1=$winfrct1;winfrct2=$winfrct2;%s$desc", ($do_hidedesc ? "" : "desc="));
}
else {
$attributes .= sprintf(";seqaccn=$seqaccn;mdlaccn=$mdlaccn;mdl=$mdl;mdlfrom=$mdlfrom;mdlto=$mdlto;trunc=$trunc;pass=$pass;gc=$gc;bias=$bias;inc=$inc;%s$desc", ($do_hidedesc ? "" : "desc="));
}
}
elsif($do_no_attributes) {
$attributes = "-";
}
elsif($do_de_attributes) {
$attributes = $desc;
}
if(defined $extra) {
if($attributes eq "-") { $attributes = ""; }
elsif($attributes !~ m/\;$/) { $attributes .= ";"; }
$attributes .= $extra . ";";
}
printf("%s\t%s\t%s\t%d\t%d\t%.1f\t%s\t%s\t%s\n",
$seqname, # token 1: 'sequence' (sequence name)
$source, # token 2: 'source'
$mdlname, # token 3: 'feature' (model name) you may want to change this to 'ncRNA'
($strand eq "+") ? $seqfrom : $seqto, # token 4: 'start' in coordinate space [1..seqlen], must be <= 'end'
($strand eq "+") ? $seqto : $seqfrom, # token 5: 'end' in coordinate space [1..seqlen], must be >= 'start'
$score, # token 6: 'score' bit score
$strand, # token 7: 'strand' ('+' or '-')
".", # token 8: 'phase' irrelevant for noncoding RNAs
$attributes); # token 9: attributes, currently only E-value, unless --all, --none or --desc
}
}
}