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#!/usr/bin/perl
use strict;
use warnings;
# Script to convert PATRIC files to 5-column feature table files.
my $tabfile = shift or die "Must supply input filename\n";
open (my $TAB_IN, $tabfile) or die "Unable to open $tabfile\n";
my $base = $tabfile;
if ($base =~ /^(.+)\.tab$/) {
$base = $1;
}
open (my $TBL_OUT, ">$base.tbl") or die "Unable to open feature table output file\n";
# define global variables
my $line_number = 0;
my $thisline;
my $show_first_line = 1;
my $from = 0;
my $to = 0;
my $strand = "+";
# skip first line with table headers
$thisline = <$TAB_IN>;
# main loop reads one line at a time
while ($thisline = <$TAB_IN>) {
$thisline =~ s/\r//;
$thisline =~ s/\n//;
$line_number++;
if ($thisline ne "") {
my @items = split ('\t', $thisline);
my $numitems = @items;
if ($numitems > 3 && $items [3] eq "source" && $show_first_line == 1) {
$show_first_line = 0;
my $accn = $items [1];
print $TBL_OUT ">Feature $accn\n";
}
if ($numitems > 8 && $items [3] eq "gene") {
my $locus_tag = $items [5];
$from = $items [6];
$to = $items [7];
$strand = $items [8];
if ($strand eq "-") {
print $TBL_OUT "$to\t$from\tgene\n";
} else {
print $TBL_OUT "$from\t$to\tgene\n";
}
print $TBL_OUT "\t\t\tlocus_tag\t$locus_tag\n";
}
if ($numitems > 11 && $items [3] eq "CDS") {
my $product = $items [11];
$from = $items [6];
$to = $items [7];
$strand = $items [8];
if ($strand eq "-") {
print $TBL_OUT "$to\t$from\tCDS\n";
} else {
print $TBL_OUT "$from\t$to\tCDS\n";
}
print $TBL_OUT "\t\t\tproduct\t$product\n";
}
}
}
# close input and output files
close ($TAB_IN);
close ($TBL_OUT);
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