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#! @PERL@
# $Id: gmap_process.pl.in,v 1.8 2010-07-21 22:02:18 twu Exp $
use warnings;
use IO::File;
use Getopt::Std;
undef($opt_c); # coord file
undef($opt_g); # gunzip each file
undef($opt_f); # File with input FASTA source filenames
getopts("c:gf:");
if (!defined($coord_file = $opt_c)) {
if (-e "coords.txt") {
$coord_file = "coords.txt";
} else {
die "Must specify coordinate file (created by md_coords or fa_coords) with -c flag."
}
}
read_coords($coord_file);
if (defined($opt_f)) {
# Source files given in a file
@sourcefiles = ();
$SOURCES = new IO::File($opt_f) or die "Cannot open file $opt_f";
while (defined($line = <$SOURCES>)) {
chop $line;
push @sourcefiles,$line;
}
close($SOURCES);
process_fasta(\@sourcefiles);
} elsif ($#ARGV < 0) {
# FASTA is piped via stdin
@streams = ();
push @streams,"<&STDIN";
process_fasta(\@streams);
} else {
# Source files given on command line
process_fasta(\@ARGV);
}
check_processed();
exit;
sub read_coords {
my ($coord_file) = @_;
my $universal_coord = 0;
$FP = new IO::File($coord_file) or die "Cannot open coord file $coord_file";
print STDERR "Reading coordinates from file $coord_file\n";
while (defined($line = <$FP>)) {
if ($line =~ /^#/) {
#if ($line =~ /Reference strain:\s*(\S+)/) {
#$refstrain = $1;
#}
} else {
$line =~ s/\r\n/\n/;
chop $line;
@fields = split /\s+/,$line;
$contig = $fields[0];
#if (!defined($strain{$contig} = $fields[2])) {
#$strain{$contig} = "";
#} elsif (defined($refstrain) && $strain{$contig} eq $refstrain) {
#$strain{$contig} = "";
#}
$coords{$contig} = $fields[1];
$universal_coord{$contig} = $universal_coord;
($chrstart,$chrend) = $coords{$contig} =~ /\S+:(\d+)\.\.(\d+)/;
if (!defined($fields[2])) {
$universal_coord += $chrend - $chrstart + 1;
} elsif ($fields[2] eq "circular") {
$circularp{$contig} = 1;
$universal_coord += $chrend - $chrstart + 1;
$universal_coord += $chrend - $chrstart + 1;
} elsif ($fields[2] eq "primary") {
# Linear and primary
$universal_coord += $chrend - $chrstart + 1;
} else {
# Altloc
$primary{$contig} = $fields[2];
$universal_coord += $chrend - $chrstart + 1;
}
}
}
close($FP);
return;
}
sub find_contig_name {
my ($contiginfo, $coords) = @_;
if ($contiginfo !~ /\|/) {
if (defined($ {$coords}{$contiginfo})) {
return $contiginfo;
} elsif ($contiginfo =~ /(\S+)/ && defined($ {$coords}{$1})) {
return $1;
} else {
# Failed
return $contiginfo;
}
} else {
# Old code for FASTA files that contained pipe delimiters
@parts = split /\|/,$contiginfo;
foreach $part (@parts) {
if (defined($ {$coords}{$part})) {
return $part;
} elsif ($part =~ /(\S+)/ && defined($ {$coords}{$1})) {
return $1;
}
}
# Failed
return $contiginfo;
}
}
sub process_fasta {
my ($argv) = @_;
my $printp = 0;
foreach $arg (@ {$argv}) {
if (defined($opt_g)) {
$FP = new IO::File("gunzip -c \"$arg\" |") or die "Cannot open file $arg";
} else {
$FP = new IO::File($arg) or die "Cannot open file $arg";
}
while (defined($line = <$FP>)) {
$line =~ s/\r\n/\n/;
chomp $line;
if ($line !~ /\S/) {
# Skip blank lines
} elsif ($line =~ /^>(\S+)/) {
# $contig = find_contig_name($1,\%coords);
$contig = $1;
if (!defined($coords{$contig})) {
print STDERR "No coordinates defined for contig $contig. Skipping.\n";
$printp = 0;
} else {
# ($chr,$chrpos1,$chrpos2) = $coords{$contig} =~ /(\S+):(\d+)\D+(\d+)/;
# If $chrpos2 < $chrpos1, then contig needs to be reverse complement.
# However, gmapindex knows how to handle this
$processedp{$contig} = 1;
#printf (">%s\t%s\t%s\n",$contig,$coords{$contig},$strain{$contig});
printf (">%s\t%s\t%u",$contig,$coords{$contig},$universal_coord{$contig});
if (defined($circularp{$contig})) {
print "\tcircular";
} elsif (defined($primary{$contig})) {
print "\t" . $primary{$contig};
}
print "\n";
$printp = 1;
}
} elsif ($printp == 1) {
print $line . "\n";
}
}
close($FP);
}
return;
}
sub check_processed {
$nwarnings = 0;
foreach $contig (keys %coords) {
if (!defined($processedp{$contig})) {
print STDERR "Warning!! Contig $contig was listed in coords file, but not seen in a FASTA file\n";
$nwarnings++;
}
}
if ($nwarnings > 0) {
print STDERR "Warning: A total of $nwarnings contigs were listed in coords file, but not seen in a FASTA file\n";
print STDERR "Should provide the correct FASTA files, or comment out these contigs in the coords file $coord_file\n";
}
return;
}
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