Parent Directory
| 
Revision Log
Revision 1.2 - (view) (download) (as text)
| 1 : | jdavis | 1.1 | #! /usr/bin/env perl |
| 2 : | use strict; | ||
| 3 : | use Data::Dumper; | ||
| 4 : | use Getopt::Long; | ||
| 5 : | use SeedEnv; | ||
| 6 : | |||
| 7 : | jdavis | 1.2 | my $usage = 'reps_for_wc.pl -n [number of genomes] -l list of PSEED IDs -o output_prefix > List of Rep IDs |
| 8 : | -l list of PSEED ids, 1 per line | ||
| 9 : | -n number of reps you want | ||
| 10 : | -o output prefix for alignment and tree files | ||
| 11 : | jdavis | 1.1 | This program |
| 12 : | 1) takes a list of PSEED ids, | ||
| 13 : | 2) extracts a set of universal genes, | ||
| 14 : | 3) builds a concatenated alignment | ||
| 15 : | 4) builds a tree | ||
| 16 : | 5) extrancts n representative tips from the tree'; | ||
| 17 : | |||
| 18 : | my ($help, $nreps, $list, $output); | ||
| 19 : | |||
| 20 : | my $rc = GetOptions('h' => \$help, | ||
| 21 : | 'l=s' => \$list, | ||
| 22 : | 'n=i' => \$nreps, | ||
| 23 : | 'o=s' => \$output); | ||
| 24 : | |||
| 25 : | if ((! $rc) || ($help)) | ||
| 26 : | { | ||
| 27 : | die $usage; | ||
| 28 : | } | ||
| 29 : | if (! $list) | ||
| 30 : | { | ||
| 31 : | die "Must provide a list of PSEED IDS with -l option\n"; | ||
| 32 : | } | ||
| 33 : | if (! $nreps) | ||
| 34 : | { | ||
| 35 : | die "must provide -n number of representatives desired\n"; | ||
| 36 : | } | ||
| 37 : | if (! $output) | ||
| 38 : | { | ||
| 39 : | die "must provide -o prefix for output files\n"; | ||
| 40 : | } | ||
| 41 : | |||
| 42 : | opendir(DIR,".") || die "could not open current working directory"; | ||
| 43 : | my @files = grep { $_ !~ /^\./ } readdir(DIR); | ||
| 44 : | foreach (@files) | ||
| 45 : | { | ||
| 46 : | if ($_ =~ /$output/) | ||
| 47 : | { | ||
| 48 : | die "File prefix, $output has already been used, please choose a different prefix\n"; | ||
| 49 : | } | ||
| 50 : | } | ||
| 51 : | |||
| 52 : | closedir(GTOS); | ||
| 53 : | |||
| 54 : | &SeedUtils::run("k-class-tree-from-contig-dir -o $output -p $list"); | ||
| 55 : | jdavis | 1.2 | &SeedUtils::run("k-class-representative_n_tree_tips -n $nreps <$output.nwk"); |
| MCS Webmaster | ViewVC Help |
| Powered by ViewVC 1.0.3 |