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annotate gd_snp2vcf.pl @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents a631c2f6d913
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
31
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1 #!/usr/bin/perl -w
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2 use strict;
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3
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4 #convert from gd_snp file to vcf file (with dbSNP fields)
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5
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6 #gd_snp table format:
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7 #1. chr
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8 #2. position (0 based)
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9 #3. ref allele
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10 #4. second allele
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11 #5. overall quality
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12 #foreach individual (6-9, 10-13, ...)
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13 #a. count of allele in 3
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14 #b. count of allele in 4
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15 #c. genotype call (-1, or count of ref allele)
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16 #d. quality of genotype call (quality of non-ref allele from masterVar)
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17
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18 if (!@ARGV) {
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19 print "usage: gd_snp2vcf.pl file.gd_snp[.gz|.bz2] -geno=8[,12:16,20...] -handle=HANDLE -batch=BATCHNAME -ref=REFERENCEID [-bioproj=XYZ -biosamp=ABC -population=POPID[,POPID2...] -chrCol=9 -posCol=9 ] > snpsForSubmission.vcf\n";
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20 exit;
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21 }
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22
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23 my $in = shift @ARGV;
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24 my $genoCols = '';
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25 my $handle;
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26 my $batch;
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27 my $bioproj;
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28 my $biosamp;
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29 my $ref;
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30 my $pop;
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31 my $cr = 0; #allow to use alternate reference?
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32 my $cp = 1;
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33 my $meta;
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34 my $offset = 0; #offset for genotype column, gd_snp vs gd_genotype indivs file
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35 foreach (@ARGV) {
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36 if (/-geno=([0-9,]+)/) { $genoCols .= "$1:"; }
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37 elsif (/-geno=(.*)/) { $genoCols .= readGeno($1); }
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38 elsif (/-off=([0-9])/) { $offset = $1; }
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39 elsif (/-handle=(.*)/) { $handle = $1; }
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40 elsif (/-batch=(.*)/) { $batch = $1; }
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41 elsif (/-bioproj=(.*)/) { $bioproj = $1; }
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42 elsif (/-biosamp=(.*)/) { $biosamp = $1; }
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43 elsif (/-ref=(.*)/) { $ref = $1; }
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44 elsif (/-population=(\S+)/) { $pop = $1; }
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45 elsif (/-chrCol=(\d+)/) { $cr = $1 - 1; }
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46 elsif (/-posCol=(\d+)/) { $cp = $1 - 1; }
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47 elsif (/-metaOut=(.*)/) { $meta = $1; }
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48 }
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49 if ($cr < 0 or $cp < 0) { die "ERROR the column numbers should be 1 based.\n"; }
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50
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51 #remove trailing delimiters
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52 $genoCols =~ s/,:/:/g;
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53 $genoCols =~ s/[,:]$//;
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54
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55 my @gnc = split(/,|:/, $genoCols);
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56
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57 if ($in =~ /.gz$/) {
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58 open(FH, "zcat $in |") or die "Couldn't open $in, $!\n";
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59 }elsif ($in =~ /.bz2$/) {
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60 open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n";
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61 }else {
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62 open(FH, $in) or die "Couldn't open $in, $!\n";
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63 }
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64 my @head = prepHeader();
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65 if (@head) {
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66 print join("\n", @head), "\n";
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67 #now column headers
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68 print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO";
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69 if (defined $pop) {
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70 $pop =~ s/,$//;
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71 my $t = $pop;
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72 $t =~ s/,/\t/g;
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73 print "\tFORMAT\t$t";
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74 }
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75 print "\n";
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76 }
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77 while (<FH>) {
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78 chomp;
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79 if (/^#/) { next; }
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80 if (/^\s*$/) { next; }
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81 my @f = split(/\t/);
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82 #vcf columns: chrom pos id ref alt qual filter info
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83 # info must have VRT=[0-9] 1==SNV 2=indel 6=NoVariation 8=MNV ...
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84 my $vrt = 1;
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85 if ($f[2] !~ /^[ACTG]$/ or $f[3] !~ /^[ACTG]$/) {
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86 die "Sorry this can only do SNV's at this time\n";
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87 }
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88 if (scalar @gnc == 1 && !defined $pop) { #single genotype column
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89 if (!defined $f[4] or $f[4] == -1) { $f[4] = '.'; }
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90 if ($f[$gnc[0]-1] == 2) { $vrt = 6; } #reference match
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91 if ($f[$gnc[0]-1] == -1) { next; } #no data, don't use
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92 print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\n";
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93 #TODO? put read counts in comment?
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94 }elsif ($pop) { #do as population
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95 my @cols;
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96 foreach my $gp (split(/:/,$genoCols)) { #foreach population
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97 my @g = split(/,/, $gp);
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98 my $totChrom = 2*(scalar @g);
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99 my $totRef = 0;
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100 foreach my $i (@g) { if (!defined $f[$i-1] or $f[$i-1] == -1) { $totChrom -= 2; next; } $totRef += $f[$i-1]; }
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101 if ($totChrom == $totRef) { $vrt = 6; }
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102 if ($totRef > $totChrom) { die "ERROR likely the wrong column was chosen for genotype\n"; }
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103 my $altCnt = $totChrom - $totRef;
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104 push(@cols, "$totChrom:$altCnt");
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105 }
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106 print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\tNA:AC\t", join("\t", @cols), "\n";
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107 }else { #leave allele counts off
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108 my $totChrom = 2*(scalar @gnc);
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109 my $totRef = 0;
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110 foreach my $i (@gnc) { if ($f[$i-1] == -1) { $totChrom -= 2; next; } $totRef += $f[$i-1]; }
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111 if ($totChrom == $totRef) { $vrt = 6; }
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112 print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\n";
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diff changeset
113 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
114 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
115 close FH or die "Couldn't close $in, $!\n";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
116
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
117 if ($meta) {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
118 open(FH, ">", $meta) or die "Couldn't open $meta, $!\n";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
119 print FH "TYPE: CONT\n",
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
120 "HANDLE: $handle\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
121 "NAME: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
122 "FAX: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
123 "TEL: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
124 "EMAIL: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
125 "LAB: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
126 "INST: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
127 "ADDR: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
128 "||\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
129 "TYPE: METHOD\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
130 "HANDLE: $handle\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
131 "ID: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
132 "METHOD_CLASS: Sequence\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
133 "TEMPLATE_TYPE: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
134 "METHOD:\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
135 "||\n";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
136 if ($pop) {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
137 my @p = split(/,/, $pop);
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
138 foreach my $t (@p) {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
139 print FH
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
140 "TYPE: POPULATION\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
141 "HANDLE: $handle\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
142 "ID: $t\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
143 "POPULATION: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
144 "||\n";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
145 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
146 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
147 print FH "TYPE: SNPASSAY\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
148 "HANDLE: $handle\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
149 "BATCH: $batch\n",
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
150 "MOLTYPE: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
151 "METHOD: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
152 "ORGANISM: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
153 "||\n",
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
154 "TYPE: SNPPOPUSE | SNPINDUSE\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
155 "HANDLE: $handle\n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
156 "BATCH: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
157 "METHOD: \n",
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
158 "||\n";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
159
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
160 close FH or die "Couldn't close $meta, $!\n";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
161 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
162
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
163 exit 0;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
164
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
165 #parse old header and add or create new
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
166 sub prepHeader {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
167 my @h;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
168 $h[0] = '##fileformat=VCFv4.1';
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
169 my ($day, $mo, $yr) = (localtime)[3,4,5];
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
170 $mo++;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
171 $yr+=1900;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
172 $h[1] = '##fileDate=' . "$yr$mo$day";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
173 $h[2] = "##handle=$handle";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
174 $h[3] = "##batch=$batch";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
175 my $i = 4;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
176 if ($bioproj) { $h[$i] = "##bioproject_id=$bioproj"; $i++; }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
177 if ($biosamp) { $h[$i] = "##biosample_id=$biosamp"; $i++; }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
178 $h[$i] = "##reference=$ref"; ##reference=GCF_999999.99
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
179 #$i++;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
180 #$h[$i] = '##INFO=<ID=LID, Number=1,Type=string, Description="Unique local variation ID or name for display. The LID provided here combined with the handle must be unique for a particular submitter.">'
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
181 $i++;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
182 $h[$i] = '##INFO=<ID=VRT,Number=1,Type=Integer,Description="Variation type,1 - SNV: single nucleotide variation,2 - DIV: deletion/insertion variation,3 - HETEROZYGOUS: variable, but undefined at nucleotide level,4 - STR: short tandem repeat (microsatellite) variation, 5 - NAMED: insertion/deletion variation of named repetitive element,6 - NO VARIATON: sequence scanned for variation, but none observed,7 - MIXED: cluster contains submissions from 2 or more allelic classes (not used) ,8 - MNV: multiple nucleotide variation with all eles of common length greater than 1,9 - Exception">';
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
183 #sometimes have allele freqs?
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
184 if (defined $pop) {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
185 $i++;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
186 $h[$i] = "##FORMAT=<ID=NA,Number=1,Type=Integer,Description=\"Number of alleles for the population.\"";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
187 $i++;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
188 $h[$i] = '##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count for each alternate allele.">';
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
189 my @p = split(/,/, $pop);
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
190 foreach my $t (@p) {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
191 $i++;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
192 $h[$i] = "##population_id=$t";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
193 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
194 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
195 #PMID?
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
196 ##INFO=<ID=PMID,Number=.,Type=Integer,Description="PubMed ID linked to variation if available.">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
197
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
198 return @h;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
199 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
200 ####End
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
201
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
202 #read genotype columns from a file
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
203 sub readGeno {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
204 my $list = shift @_;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
205 my @files = split(/,/, $list);
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
206 my $cols='';
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
207 foreach my $file (@files) {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
208 open(FH, $file) or die "Couldn't read $file, $!\n";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
209 while (<FH>) {
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
210 chomp;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
211 my @f = split(/\s+/);
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
212 if ($f[0] =~/\D/) { die "ERROR expect an integer for the column\n"; }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
213 $f[0] += $offset;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
214 $cols .= "$f[0],";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
215 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
216 close FH;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
217 $cols .= ":";
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
218 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
219 $cols =~ s/,:$//;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
220 return $cols;
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
221 }
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
222 ####End