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sort mgaps file before postpro. (on behalf of @jerviedog - fixes #55 … #94

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sort mgaps file before postpro. (on behalf of @jerviedog - fixes #55 … #94

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66 changes: 66 additions & 0 deletions scripts/promer.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -346,6 +346,8 @@ ( )

#-- Run postpro and assert return value is zero
print (STDERR "4: FINISHING DATA\n");
sort_mgaps("$qry_file","$pfx.mgaps");

$err[0] = $tigr->runCommand
("$postpro_path $psw -x $blsm -b $blen ".
"$ref_file $qry_file $pfx < $pfx.mgaps");
Expand Down Expand Up @@ -379,4 +381,68 @@ ( )

exit ( main ( ) );

sub sort_mgaps {
# Input, file names, strings
my $qry = shift;
my $mgaps = shift;
# read query file
my @qry_entries = ();
my $fh;
open($fh, "$qry") || die "couldn't read file $qry\n";
while(my $line = <$fh>) {
chomp $line;
next unless $line=~/^\>(\S+)/;
push(@qry_entries,$1);
}
close($fh);
# read mgaps file
my %mgaps_lines = ();
my %dna_pep = (); # used to look up the peptides in a dna seq
open($fh, "$mgaps") || die "couldn't read file $mgaps\n";
my $pos = 0;
my $pos_old = $pos;
my $cur_entry = ""; # e.g. 3210101.5
while(1) {
my $line=<$fh>;
last unless defined $line;
chomp $line;
if($line=~/^\>\s*(\S+)/) {
$cur_entry = $1;
# find out the corresponding dna id in query file
die "wrong format $cur_entry\n"
unless $cur_entry=~/^(.+)\.[\d+]$/;
my $dna = $1;
if(exists($dna_pep{$dna})) {
push(@{$dna_pep{$dna}},$cur_entry);
}
else {
$dna_pep{$dna} = [$cur_entry];
}
# find out the lines corresponding to the current entry
if(exists($mgaps_lines{$cur_entry})) {
push(@{$mgaps_lines{$cur_entry}},"$line\n");
}
else {
$mgaps_lines{$cur_entry} = ["$line\n"];
}
}
else {
push(@{$mgaps_lines{$cur_entry}},"$line\n");
}
}
close($fh);
# sort the query file
open($fh,">$mgaps") || die "couldn't write to file $mgaps\n";
my $oldfh = select($fh);
foreach my $dna (@qry_entries) {
foreach my $pep (@{$dna_pep{$dna}}) {
my $ref_line = $mgaps_lines{$pep};
foreach my $line(@{$ref_line}) {
print $line;
}
}
}
select($oldfh);
close($fh);
}
#-- END OF SCRIPT