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Revision 1.1 - (view) (download) (as text)
| 1 : | overbeek | 1.1 | use strict; |
| 2 : | use Data::Dumper; | ||
| 3 : | use Getopt::Long; | ||
| 4 : | |||
| 5 : | my $usage = "usage: pg_add_genomes -d Data\n"; | ||
| 6 : | my $dataD; | ||
| 7 : | |||
| 8 : | my $rc = GetOptions('d=s' => \$dataD); | ||
| 9 : | if ((! $rc) || (! -d $dataD)) { print STDERR $usage; exit } | ||
| 10 : | |||
| 11 : | open(OUT,">$dataD/genomes.with.job.and.genomeID") | ||
| 12 : | || die "could not open $dataD/genomes.with.job.and.genomeID"; | ||
| 13 : | |||
| 14 : | foreach $_ (`cat $dataD/genomes.with.job`) | ||
| 15 : | { | ||
| 16 : | chop; | ||
| 17 : | my @flds = split(/\t/,$_); | ||
| 18 : | my $rast_job = $flds[-1]; | ||
| 19 : | my $jobD = "/vol/rast-prod/jobs/$rast_job/rp"; | ||
| 20 : | opendir(D,$jobD) || die $jobD; | ||
| 21 : | my @tmp = grep { $_ =~ /^\d+\.\d+$/ } readdir(D); | ||
| 22 : | closedir(D); | ||
| 23 : | my $genome = $tmp[0]; | ||
| 24 : | print OUT join("\t",(@flds,$genome)),"\n"; | ||
| 25 : | } | ||
| 26 : | close(OUT); |
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