Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate alignment/seqfill.pl @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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1 #!/usr/bin/perl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 my $file = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $q_mark = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 my $hyphen = $ARGV[2];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 my $N = $ARGV[3];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 my $usePartFile = $ARGV[4];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 my $partFile = $ARGV[5];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 my $out = "out.phylipnon"; # output file
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11
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 open(FILE, $file);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my @speciesNames;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 my @sequenceLines;
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15
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 my @currentLineContent;
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17
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 my $i = 0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 while($currentLine = <FILE>) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 chomp($currentLine);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 @currentLineContent = split(/\t/, $currentLine);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 $speciesNames[$i] = $currentLineContent[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 $sequenceLines[$i] = $currentLineContent[1];
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24 $i++;
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25 }
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26
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 my $dataInfo = $speciesNames[1]; # gets num of species and sequence length
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28 my @numbers = split(/ /, $dataInfo);
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29
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30 my $numberOfSpecies = $numbers[0];
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31 my $sequenceLength = $numbers[1];
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32
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33 close(FILE);
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34
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35 open(OUT, '>'.$out);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 my @columnData; # this will have $sequenceLength elements
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37 for($j = 0; $j < $numberOfSpecies+2; $j++) {
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38 for($k = 0; $k < $sequenceLength; $k++) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 $currChar = substr($sequenceLines[$j], $k, 1);
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40 $columnData[$k] = $columnData[$k].$currChar;
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41 }
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42 }
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43
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 # mark locations that will be removed
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 my @flagMap;
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46 for($i = 0; $i < $sequenceLength; $i++) {
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47 $flagMap[$i] = 0;
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48 }
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49 my $index = 0;
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50 foreach $el(@columnData) {
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51 my $tot = 0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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52 my $q_mark_occur = 0;
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53 my $hyphen_occur = 0;
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54 my $N_occur = 0;
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55
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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56 if($q_mark eq "true") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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57 $q_mark_occur = ($el =~ tr/?//);
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58 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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59 if($hyphen eq "true") {
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60 $hyphen_occur = ($el =~ tr/-//);
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61 }
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62 if($N eq "true") {
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63 $N_occur = ($el =~ tr/N//);
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64 }
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65
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66 $tot = $q_mark_occur + $hyphen_occur + $N_occur;
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67 if($tot == $numberOfSpecies) {
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68 $flagMap[$index] = 1;
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69 }
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70 $index++;
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71 }
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72
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73 my $newSequenceLength = $sequenceLength;
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74 foreach $el(@flagMap) {
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75 if($el == 1) {
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76 $newSequenceLength--;
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77 }
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78 }
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79
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80 print OUT $speciesNames[0]."\n";
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81 print OUT $numberOfSpecies." ".$newSequenceLength."\n";
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82 for($i = 2; $i < $numberOfSpecies+3; $i++) {
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83 print OUT $speciesNames[$i]."\t";
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84 for($j = 0; $j < $sequenceLength; $j++) {
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85 if($flagMap[$j] == 0) {
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86 my $character = substr($sequenceLines[$i], $j, 1);
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87 print OUT $character;
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88 }
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89 }
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90 print OUT "\n";
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91 }
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92
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93 close(OUT);
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94
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95 my $partOut = "partOut.txt";
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96
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97 if($usePartFile eq "true") {
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98 # update the partition file
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99 open(PART, $partFile);
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100 my @data;
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101 my @ranges;
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102 my @names;
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103 $i = 0;
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104 while($currentLine = <PART>) {
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105 @data = split(/=/, $currentLine);
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106 $names[$i] = $data[0];
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107 $ranges[$i] = $data[1];
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108 $i++;
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109 }
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110 close(PART);
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111
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112 my $firstFlag = 1;
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113 open(PARTOUT, '>'.$partOut);
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114 $j = 0;
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115 my $newLower;
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116 foreach $el(@ranges) {
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117 print PARTOUT $names[$j]." = ";
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118 @lowerUpper = split(/-/, $el);
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119 if($firstFlag == 1) {
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120 $newLower = $lowerUpper[0];
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121 $firstFlag = 0;
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122 }
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123 my $currUpper = $lowerUpper[1];
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124 my $newUpper = $currUpper;
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125
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126
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127
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128 for($i = $currLower; $i < $currUpper; $i++) {
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129 if($flagMap[$i] == 1) {
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130 $newUpper--;
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131 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
132 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
133
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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134 print PARTOUT $newLower." - ".$newUpper."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
135 $newLower = $newUpper + 1;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
136 $j++;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
137 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
138 close(PARTOUT);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
139 }