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| 1 : | redwards | 1.1 | #__perl-- |
| 2 : | |||
| 3 : | # rewrite and merge peg.synonyms file with a partial file. For example, after adding a genome, you might run sims_after_adding_genome which then creates a partial sims file | ||
| 4 : | # this will take that file, and the existing peg.synonyms file and merge them. | ||
| 5 : | # | ||
| 6 : | # Rob Edwards | ||
| 7 : | # Nov 11, 2009 | ||
| 8 : | |||
| 9 : | use strict; | ||
| 10 : | use Getopt::Std; | ||
| 11 : | my %opts; | ||
| 12 : | getopts('n:o:d:', \%opts); | ||
| 13 : | unless ($opts{n} && $opts{o} && $opts{d}) { | ||
| 14 : | die <<EOF; | ||
| 15 : | $0 | ||
| 16 : | -n new peg synonyms that will be appended to old ones | ||
| 17 : | -o directory where old peg synonyms file is | ||
| 18 : | -d directory where new peg synonyms should end up | ||
| 19 : | EOF | ||
| 20 : | } | ||
| 21 : | |||
| 22 : | unless (-e "$opts{o}/peg.synonyms") {die "OLD FILE: $opts{o}/peg.synonyms does not exist!"} | ||
| 23 : | unless (-e "$opts{n}") {die "NEW FILE: $opts{n} does not exist!"} | ||
| 24 : | if (-e "$opts{d}/peg.synonyms") {die "Cowardly won't overwrite $opts{d}/peg.synonyms"} | ||
| 25 : | |||
| 26 : | open(IN, $opts{n}) || die "can't open $opts{n}"; | ||
| 27 : | my $line; | ||
| 28 : | while (<IN>) { | ||
| 29 : | chomp; | ||
| 30 : | my ($md5, $matches)=split /\t/; | ||
| 31 : | foreach my $tple (split /\;/, $matches) { | ||
| 32 : | my ($peg, $len)=split /\,/, $tple; | ||
| 33 : | $line->{$md5}->{$peg}=$len; | ||
| 34 : | } | ||
| 35 : | } | ||
| 36 : | close IN; | ||
| 37 : | |||
| 38 : | open(IN, "$opts{o}/peg.synonyms") || die "can't open $opts{o}/peg.synonyms"; | ||
| 39 : | open(OUT, ">$opts{d}/peg.synonyms") || die "can't write to $opts{d}/peg.synonyms"; | ||
| 40 : | while (<IN>) { | ||
| 41 : | my ($md5, $matches)=split /\t/; | ||
| 42 : | if ($line->{$md5}) { | ||
| 43 : | chomp($matches); | ||
| 44 : | foreach my $tple (split /\;/, $matches) { | ||
| 45 : | my ($peg, $len)=split /\,/, $tple; | ||
| 46 : | $line->{$md5}->{$peg}=$len; | ||
| 47 : | } | ||
| 48 : | } | ||
| 49 : | else { | ||
| 50 : | print OUT; | ||
| 51 : | } | ||
| 52 : | } | ||
| 53 : | foreach my $md5 (keys %$line) { | ||
| 54 : | print OUT "$md5\t", join(";", map {$_="$_,".$line->{$md5}->{$_}} keys %{$line->{$md5}}), "\n"; | ||
| 55 : | } | ||
| 56 : | close IN; | ||
| 57 : | close OUT; | ||
| 58 : |
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