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Revision 1.1 - (view) (download) (as text)
| 1 : | parrello | 1.1 | =head1 Fix Up a Package Directory Containing Binning Files |
| 2 : | |||
| 3 : | package_fix.pl [options] targetDir | ||
| 4 : | |||
| 5 : | This script fixes up genome packages created from bins using files downloaded from a PATRIC binning run. The L<package_genome.pl> | ||
| 6 : | script should already have been run on the genomes. For each package directory I<XXXXXX.X>, there should be three files in the | ||
| 7 : | target directory. | ||
| 8 : | |||
| 9 : | =over 4 | ||
| 10 : | |||
| 11 : | =item 1 | ||
| 12 : | |||
| 13 : | I<XXXXXX.X>C<.scikit.eval.txt> becomes I<XXXXXX.X>C</EvalBySciKit/evaluate.out> | ||
| 14 : | |||
| 15 : | =item 2 | ||
| 16 : | |||
| 17 : | I<XXXXXX.X>C<.scikit.txt> becomes I<XXXXXX.X>C</EvalBySciKit/evaluate.log> | ||
| 18 : | |||
| 19 : | =item 3 | ||
| 20 : | |||
| 21 : | I<XXXXXX.X>C<.checkm.txt> becomes I<XXXXXX.X>C</EvalByCheckM/evaluate.log> | ||
| 22 : | |||
| 23 : | =back | ||
| 24 : | |||
| 25 : | |||
| 26 : | |||
| 27 : | =head2 Parameters | ||
| 28 : | |||
| 29 : | The sole positional parameter is the name of the target directory. | ||
| 30 : | |||
| 31 : | =cut | ||
| 32 : | |||
| 33 : | use strict; | ||
| 34 : | use P3DataAPI; | ||
| 35 : | use P3Utils; | ||
| 36 : | use File::Copy::Recursive; | ||
| 37 : | |||
| 38 : | # Get the command-line options. | ||
| 39 : | my $opt = P3Utils::script_opts('targetDir'); | ||
| 40 : | my ($targetDir) = @ARGV; | ||
| 41 : | if (! $targetDir) { | ||
| 42 : | die "No target directory specified."; | ||
| 43 : | } elsif (! -d $targetDir) { | ||
| 44 : | die "Target directory not found or invalid."; | ||
| 45 : | } | ||
| 46 : | # Read the files and directories in the target dir. | ||
| 47 : | opendir(my $dh, $targetDir) || die "Could not open $targetDir: $!"; | ||
| 48 : | my (@packages, %outFiles); | ||
| 49 : | while (my $member = readdir $dh) { | ||
| 50 : | if ($member =~ /^\d+\.\d+$/) { | ||
| 51 : | push @packages, $member; | ||
| 52 : | } elsif ($member =~ /\.txt$/) { | ||
| 53 : | $outFiles{$member} = 1; | ||
| 54 : | } | ||
| 55 : | } | ||
| 56 : | closedir $dh; | ||
| 57 : | print scalar(@packages) . " package directories found.\n"; | ||
| 58 : | # Loop through the packages. | ||
| 59 : | for my $pkg (@packages) { | ||
| 60 : | print "Checking package $pkg.\n"; | ||
| 61 : | if ($outFiles{"$pkg.scikit.eval.txt"} && $outFiles{"$pkg.scikit.txt"} && $outFiles{"$pkg.checkm.txt"}) { | ||
| 62 : | print "Eval files found for $pkg.\n"; | ||
| 63 : | # We have the files. Move them. | ||
| 64 : | File::Copy::Recursive::fmove("$targetDir/$pkg.scikit.eval.txt", "$targetDir/$pkg/EvalBySciKit/evaluate.out") || die "Could not move scikit.eval.txt: $!"; | ||
| 65 : | File::Copy::Recursive::fmove("$targetDir/$pkg.scikit.txt", "$targetDir/$pkg/EvalBySciKit/evaluate.log") || die "Could not move scikit.txt: $!"; | ||
| 66 : | File::Copy::Recursive::fmove("$targetDir/$pkg.checkm.txt", "$targetDir/$pkg/EvalByCheckm/evaluate.log") || die "Could not move checkm.txt: $!"; | ||
| 67 : | print "Files moved.\n"; | ||
| 68 : | } | ||
| 69 : | } |
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