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tmp.id_index.pl
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tmp.id_index.pl
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#!/usr/bin/env perl
###########################################################################
# Create id index for NCBI bactera genomes
#
# Input: GFF, PTT, FFN, FAA files
#
# Ouput: table contain id index for all genes
#
# Wang Ming wangmcas(AT)gmail.com
###########################################################################
use strict;
use warnings;
use File::Basename qw(basename dirname);
use File::Spec::Functions qw(catfile);
use File::Path qw(make_path);
use Getopt::Std;
use Data::Dumper;
id_index();
exit(1);
### subroutines
sub id_index {
my %opts = ();
getopts("o:", \%opts);
usage() if(@ARGV != 1);
my $in = shift(@ARGV);
my %ptt = %{read_ptt($in)};
die("[$in] not like a PTT file\n") if((keys %ptt) < 1 || ! $in =~ /\.ptt$/);
my $strain = `head -n1 $in`;
$strain = (split /\-/, $strain)[0] if($strain =~ /\-/);
### parse other 3 files
my ($g_name) = basename($in) =~ /(.*)\.ptt$/;
my $outdir = $g_name . "_index";
$outdir = $opts{o} if(defined $opts{o});
make_path($outdir) if(! -d $outdir);
my $GFF = catfile(dirname($in), $g_name . ".gff");
my $FFN = catfile(dirname($in), $g_name . ".ffn");
my $FAA = catfile(dirname($in), $g_name . ".faa");
die("[$in] file not exists\n") if(! -e $in);
die("[*.gff, *.ffn, *.faa] missing some files\n") if(! -e $GFF || ! -e $FFN || ! -e $FAA);
my %gff = %{read_gff($GFF)};
my %ffn = %{read_ffn($FFN)};
my %faa = %{read_faa($FAA)};
#
my $gene_diff_pro = '';
my $ffn_nothit = '';
my $faa_nothit = '';
my $report_gff = 0;
my $report_ptt = 0;
my $report_dna = 0;
my $report_pro = 0;
my $dna = catfile($outdir, $g_name . "_dna.fa");
my $pro = catfile($outdir, $g_name . "_pro.fa");
my $outidx = catfile($outdir, $g_name . "_index.txt");
open my $fh_dna, "> $dna" or die "Cannot write to $dna, $!\n";
open my $fh_pro, "> $pro" or die "Cannot write to $pro, $!\n";
open my $fh_idx, "> $outidx" or die "Cannot write to $outidx, $!\n";
for my $i (sort keys %{$ptt{index}}) {
my ($id, $name, $length, $start, $end, $strand, $pid, $cog, $des) = split /\t/, $ptt{index}->{$i};
### search GFF
my ($chr, $GeneID) = ('-', '-');
if (exists $gff{index}->{$i}) {
($id, $chr, $length, $start, $end, $strand, $GeneID) = split /\t/, $gff{index}->{$i};
delete $gff{index}->{$i};
$report_gff ++;
}elsif(exists $gff{locus}->{$id}) {
### output the records, gene and CDS have different coordinations
my @tabs = split /\t/, $gff{locus}->{$id};
$gene_diff_pro .= join("\t", @tabs[0..5], $id, $tabs[1], $length, $start, $end, $strand, $des) . "\n";
($id, $chr, $length, $start, $end, $strand, $GeneID) = @tabs;
$report_gff ++;
}else {
warn("[$id] not found in GFF file\n");
}
### search FFN
my $ffn_id = '-';
my $ffn_fa = '';
if(exists $ffn{$i}) {
($ffn_id, $ffn_fa) = split /\t/, $ffn{$i};
print $fh_dna '>' . $id . "\n" . $ffn_fa . "\n";
delete $ffn{$i};
$report_dna ++;
}else {
$ffn_nothit .= join("\t", $id, $chr, $length, $start, $end, $strand, $des) . "\n";
# die("[$id] not found in FFN file\n");
}
my $faa_id = '-';
my $faa_fa = '';
if(exists $faa{$pid}) {
($faa_id, $faa_fa) = split /\t/, $faa{$pid};
print $fh_pro '>' . $id . "\n" . $faa_fa . "\n";
delete $faa{$pid};
$report_pro ++;
}else {
$faa_nothit .= join("\t", $id, $chr, $length, $start, $end, $strand, $des) . "\n";
# die("[$id] not found in FAA file\n");
}
### output : output the gene coordinations according to GFF file
print $fh_idx join("\t", $id, $chr, $length, $start, $end, $strand, $name, $GeneID,
$pid, $cog, $ffn_id, $faa_id, $des) . "\n";
$report_ptt ++;
}
close $fh_dna;
close $fh_pro;
close $fh_idx;
### validation
### report
my $report_file = catfile($outdir, $g_name . '_report.txt');
open my $fh_rpt, "> $report_file" or die "Cannot write to $report_file, $!\n";
my $report_line = ">$g_name" . ': ' . $strain . "\n";
$report_line .= 'Find entries in PTT:' . "\t" . $report_ptt . "\n";
$report_line .= 'Find entries in FFN:' . "\t" . $report_dna . "\n";
$report_line .= 'Find entries in FAA:' . "\t" . $report_pro . "\n";
$report_line .= "\n" . 'The following gene(*.FFN) and CDS(*.FAA) are differ in coordinations:' . "\n";
$report_line .= join("\t", '#g.id', 'Chr', 'g.length', 'g.start', 'g.end', 'g.strand',
'p.id', 'Chr', 'p.length', 'p.start', 'p.end', 'p.strand', 'product') . "\n";
$report_line .= $gene_diff_pro . "\n";
$report_line .= "\n" . 'The following gene(s) are not found in FFN' . "\n";
$report_line .= $ffn_nothit . "\n";
$report_line .= "\n" . 'The following gene(s) are not found in FAA' . "\n";
$report_line .= $faa_nothit . "\n";
print $report_line;
print $fh_rpt $report_line;
close $fh_rpt;
}
### read GFF
sub read_gff {
my $in = $_[0];
my %gff = ();
open my $fh_in, "< $in" or die "Cannot open $in, $!\n";
while(<$fh_in>) {
chomp;
next if(/^\#|^\s*$/);
next unless(/\tgene\t/);
my $id = '';
my $GeneID = '-';
my @tabs = split /\t/, $_;
my $des = $tabs[8];
if(($id) = $des =~ /locus_tag=(\w+\.*\w+)/){ ### WARN: multiple locus_tags
}elsif(($id) = $des =~ /Name=(\w+)/){
}elsif(($id) = $des =~ /ID=gene\:(\w+)/){
}else{
}
if(($GeneID) = $des =~ /GeneID\:(\d+)/){};
# option
my $chr = $tabs[0];
my $start = $tabs[3];
my $end = $tabs[4];
my $length = $end - $start + 1;
my $strand = $tabs[6];
my $index = join("\:", $start, $end, $strand);
my $out = join("\t", $id, $chr, $length, $start, $end, $strand, $GeneID);
$gff{index}->{$index} = $out;
$gff{locus}->{$id} = $out;
}
close $fh_in;
return(\%gff);
}
### read PTT
sub read_ptt {
my $in = $_[0];
my %ptt = ();
open my $fh_in, "< $in" or die "Cannot open $in, $!\n";
while(<$fh_in>) {
chomp;
next if(/^\#|^\s+$/);
next unless(/^\d+\.\.\d+\t/);
my @tabs = split /\t/, $_;
my ($start, $end) = split /\.+/, $tabs[0];
my $length = $end - $start + 1;
my $strand = $tabs[1];
my $pid = $tabs[3];
my $name = $tabs[4];
my $id = $tabs[5];
my $cog = $tabs[7];
my $des = $tabs[8];
my $index = join("\:", $start, $end, $strand);
$ptt{index}->{$index} = join("\t", $id, $name, $length, $start, $end, $strand, $pid, $cog, $des);
# $ptt{pid}->{$pid} = join("\t", $id, $name, $length, $start, $end, $strand, $pid, $cog, $des);
}
close $fh_in;
return(\%ptt);
}
### read FFN
sub read_ffn {
my $in = $_[0];
my %ffn = ();
open my $fh_in, "< $in" or die "Cannot open $in, $!\n";
my @lines = <$fh_in>;
close $fh_in;
my @tabs = split /\>/, join("", @lines);
shift(@tabs);
for my $i (@tabs) {
my @aa = split /\n/, $i;
my $header = shift(@aa);
my $fa = join("\n", @aa);
my $ffn_id = (split /\s/, $header)[0];
my ($a, $b) = $ffn_id =~ /\:(\w+)\-(\d+)/;
my ($start, $end, $strand) = ($a, $b, '+');
if($a =~ /^[a-z]/) {
($start) = $a =~ /(\d+)/;
$end = $b;
$strand = '-';
}
($start, $end) = ($end, $start) if($start > $end);
my $index = join("\:", $start, $end, $strand);
$ffn{$index} = join("\t", $ffn_id, $fa);
}
return(\%ffn);
}
### read FAA
sub read_faa {
my $in = $_[0];
my %faa = ();
open my $fh_in, "< $in" or die "Cannot open $in, $!\n";
my @lines = <$fh_in>;
close $fh_in;
my @tabs = split /\>/, join("", @lines);
shift(@tabs);
for my $i (@tabs) {
my @bb = split /\n/, $i;
my $header = shift(@bb);
my $fa = join("\n", @bb);
my $faa_id = (split /\s/, $header)[0];
my ($pid, $np) = (split /\|/, $faa_id)[1,3];
$faa{$pid} = join("\t", $faa_id, $fa);
}
return(\%faa);
}
sub usage {
die("
Usage: bac_index.pl [options] <in.ptt>
Options: -o <STR> : save results to directory
<in.ptt> : contain GFF, FFN, FAA in the same directory
Output:
1. a script to retrieve id and sequence: input <GeneID, Locus, Name ...>, output <ID, sequence>
2. id_index.table
\n");
}