[Nelsonlab-cmts] dev-boconnor/project_logic_analysis/scripts count_vgl_output_columns.pl,NONE,1.1 fix_testset_annotations.pl,NONE,1.1 fix_testset_t-cell_annotations.pl,NONE,1.1 mkdir_data_dir.sh,NONE,1.1 test_row_length.pl,NONE,1.1

[<boc...@su...>]

Update of /cvsroot/dev-boconnor/project_logic_analysis/scripts
In directory sumo.genetics.ucla.edu:/tmp/cvs-serv8351/scripts

Added Files:
	count_vgl_output_columns.pl fix_testset_annotations.pl 
	fix_testset_t-cell_annotations.pl mkdir_data_dir.sh 
	test_row_length.pl 
Log Message:
Many updates to the existing logic analysis libs and also a lot of new addtions particularly scripts


--- NEW FILE: fix_testset_t-cell_annotations.pl ---
#!/usr/local/bin/perl

use Storable;

my ($file_list, $sif_storable) = @ARGV;

my $data = retrieve($sif_storable);

open INPUT, $file_list or die;
while(<INPUT>) {
  chomp;
  print "$_\t";
  if ($data->{files}{$_}{TAL_R}) { print "TAL_R\n"; }
  else { print "HOX_R\n"; }
}

--- NEW FILE: mkdir_data_dir.sh ---
#!/bin/sh

mkdir $1
mkdir $1/hypergeometric
mkdir $1/sif
mkdir $1/analysis
# this should actually be checked in and a symlink
mkdir -p $1/analysis/templates
mkdir $1/analysis/classifications
mkdir $1/mas5
mkdir $1/ppla_output
mkdir $1/ppla_output/100
mkdir $1/profiles
mkdir $1/rand_file_lists
mkdir $1/top_profiles
mkdir $1/visualization
mkdir $1/vgl_output
# need to add sym link to dirs
mkdir $1/vgl


--- NEW FILE: test_row_length.pl ---
use Data::Dumper;

my $length = shift;

$data = {};
while(<STDIN>) {
  my @tokens = split /\s+/;
  $data->{scalar(@tokens)}++;
  if (scalar(@tokens) != $length) { print scalar(@tokens)."\t".$_; }
}

print Dumper($data);



--- NEW FILE: count_vgl_output_columns.pl ---
while(<STDIN>) {
 chomp;
 my @tokens = split /\t/;
 $i=0;
 foreach $token (@tokens) {
  #if ($token =~ /DLDA_MTtoRest_DLDA_MT_vs_DLDA_WT/) { print "$token $i\n"; }
  if ($token =~ /selected/) { print "$token $i\n"; }
  $i++;
 }
 last;
}


--- NEW FILE: fix_testset_annotations.pl ---
#!/usr/local/bin/perl

use Storable;

my ($file_list, $sif_storable) = @ARGV;

my $data = retrieve($sif_storable);

open INPUT, $file_list or die;
while(<INPUT>) {
  chomp;
  print "$_\t";
  if ($data->{files}{$_}{dlda_mt}) { print "dlda_mt\n"; }
  else { print "dlda_wt\n"; }
}