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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:SequenceFileUtil.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
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| 8 <br/> | |
| 9 <center> | |
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| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-SequenceFileUtil-"></a> 1 <span class="k">package </span><span class="i">SequenceFileUtil</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: SequenceFileUtil.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span> | |
| 18 5 <span class="c"># $Revision: 1.33 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> | |
| 47 34 | |
| 48 35 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> | |
| 49 36 | |
| 50 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> | |
| 51 38 <span class="i">@EXPORT</span> = <span class="q">qw(AreSequenceLengthsIdentical CalcuatePercentSequenceIdentity CalculatePercentSequenceIdentityMatrix GetLongestSequence GetShortestSequence GetSequenceLength IsGapResidue IsSupportedSequenceFile IsClustalWSequenceFile IsPearsonFastaSequenceFile IsMSFSequenceFile ReadSequenceFile RemoveSequenceGaps RemoveSequenceAlignmentGapColumns WritePearsonFastaSequenceFile)</span><span class="sc">;</span> | |
| 52 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 53 40 | |
| 54 41 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
| 55 42 | |
| 56 43 <span class="c"># Compare lengths of all sequences...</span> | |
| 57 <a name="AreSequenceLengthsIdentical-"></a> 44 <span class="k">sub </span><span class="m">AreSequenceLengthsIdentical</span> <span class="s">{</span> | |
| 58 45 <span class="k">my</span><span class="s">(</span><span class="i">$SequencesDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 59 46 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$FirstID</span><span class="cm">,</span> <span class="i">$FirstSeqLen</span><span class="cm">,</span> <span class="i">$FirstDifferentLenID</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="s">)</span><span class="sc">;</span> | |
| 60 47 | |
| 61 48 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> | |
| 62 49 <span class="i">$FirstID</span> = <span class="q">''</span><span class="sc">;</span> | |
| 63 50 <span class="i">$FirstDifferentLenID</span> = <span class="q">''</span><span class="sc">;</span> | |
| 64 51 | |
| 65 52 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequencesDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 66 53 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FirstID</span><span class="s">)</span> <span class="s">{</span> | |
| 67 54 <span class="i">$FirstID</span> = <span class="i">$ID</span><span class="sc">;</span> | |
| 68 55 <span class="i">$FirstSeqLen</span> = <span class="k">length</span><span class="s">(</span><span class="i">$SequencesDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="s">)</span><span class="sc">;</span> | |
| 69 56 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> | |
| 70 57 <span class="s">}</span> | |
| 71 58 <span class="i">$SeqLen</span> = <span class="k">length</span><span class="s">(</span><span class="i">$SequencesDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="s">)</span><span class="sc">;</span> | |
| 72 59 <span class="k">if</span> <span class="s">(</span><span class="i">$SeqLen</span> != <span class="i">$FirstSeqLen</span><span class="s">)</span> <span class="s">{</span> | |
| 73 60 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 74 61 <span class="i">$FirstDifferentLenID</span> = <span class="i">$ID</span><span class="sc">;</span> | |
| 75 62 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span> | |
| 76 63 <span class="s">}</span> | |
| 77 64 <span class="s">}</span> | |
| 78 65 <span class="k">return</span> <span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 79 66 <span class="s">}</span> | |
| 80 67 | |
| 81 68 <span class="c"># Calculate percent identity between two sequences. By default, gaps are ignored.</span> | |
| 82 <a name="CalcuatePercentSequenceIdentity-"></a> 69 <span class="k">sub </span><span class="m">CalcuatePercentSequenceIdentity</span> <span class="s">{</span> | |
| 83 70 <span class="k">my</span><span class="s">(</span><span class="i">$Sequence1</span><span class="cm">,</span> <span class="i">$Sequence2</span><span class="cm">,</span> <span class="i">$PercentIdentity</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span><span class="sc">;</span> | |
| 84 71 | |
| 85 72 <span class="i">$PercentIdentity</span> = <span class="q">''</span><span class="sc">;</span> | |
| 86 73 <span class="i">$Precision</span> = <span class="n">1</span><span class="sc">;</span> | |
| 87 74 <span class="i">$IgnoreGaps</span> = <span class="n">1</span><span class="sc">;</span> | |
| 88 75 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">4</span><span class="s">)</span> <span class="s">{</span> | |
| 89 76 <span class="s">(</span><span class="i">$Sequence1</span><span class="cm">,</span> <span class="i">$Sequence2</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 90 77 <span class="s">}</span> | |
| 91 78 <span class="k">elsif</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> | |
| 92 79 <span class="s">(</span><span class="i">$Sequence1</span><span class="cm">,</span> <span class="i">$Sequence2</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 93 80 <span class="s">}</span> | |
| 94 81 <span class="k">elsif</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 95 82 <span class="s">(</span><span class="i">$Sequence1</span><span class="cm">,</span> <span class="i">$Sequence2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 96 83 <span class="s">}</span> | |
| 97 84 <span class="k">else</span> <span class="s">{</span> | |
| 98 85 <span class="k">return</span> <span class="i">$PercentIdentity</span><span class="sc">;</span> | |
| 99 86 <span class="s">}</span> | |
| 100 87 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Sequence1</span><span class="s">)</span> && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Sequence2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 101 88 <span class="k">return</span> <span class="i">$PercentIdentity</span><span class="sc">;</span> | |
| 102 89 <span class="s">}</span> | |
| 103 90 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Identity</span><span class="cm">,</span> <span class="i">$Sequence1Len</span><span class="cm">,</span> <span class="i">$Sequence2Len</span><span class="cm">,</span> <span class="i">$Residue1</span><span class="cm">,</span> <span class="i">$Residue2</span><span class="cm">,</span> <span class="i">$ResMatchCount</span><span class="cm">,</span> <span class="i">$ResCount</span><span class="s">)</span><span class="sc">;</span> | |
| 104 91 | |
| 105 92 <span class="i">$Sequence1Len</span> = <span class="k">length</span><span class="s">(</span><span class="i">$Sequence1</span><span class="s">)</span><span class="sc">;</span> | |
| 106 93 <span class="i">$Sequence2Len</span> = <span class="k">length</span><span class="s">(</span><span class="i">$Sequence2</span><span class="s">)</span><span class="sc">;</span> | |
| 107 94 | |
| 108 95 <span class="i">$ResMatchCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 109 96 <span class="i">$ResCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 110 97 <span class="j">RESIDUE:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$Sequence1Len</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 111 98 <span class="i">$Residue1</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Sequence1</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 112 99 <span class="i">$Residue2</span> = <span class="s">(</span><span class="i">$Index</span> < <span class="i">$Sequence2Len</span><span class="s">)</span> ? <span class="k">substr</span><span class="s">(</span><span class="i">$Sequence2</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> | |
| 113 100 <span class="k">if</span> <span class="s">(</span><span class="i">$IgnoreGaps</span><span class="s">)</span> <span class="s">{</span> | |
| 114 101 <span class="k">if</span> <span class="s">(</span><span class="i">$Residue1</span> !~ <span class="q">/[A-Z]/i</span> || <span class="i">$Residue2</span> !~ <span class="q">/[A-Z]/i</span><span class="s">)</span> <span class="s">{</span> | |
| 115 102 <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span> | |
| 116 103 <span class="s">}</span> | |
| 117 104 <span class="s">}</span> | |
| 118 105 <span class="k">if</span> <span class="s">(</span><span class="i">$Residue1</span> <span class="k">eq</span> <span class="i">$Residue2</span><span class="s">)</span> <span class="s">{</span> | |
| 119 106 <span class="i">$ResMatchCount</span>++<span class="sc">;</span> | |
| 120 107 <span class="s">}</span> | |
| 121 108 <span class="i">$ResCount</span>++<span class="sc">;</span> | |
| 122 109 <span class="s">}</span> | |
| 123 110 <span class="i">$Identity</span> = <span class="i">$ResCount</span> ? <span class="s">(</span><span class="i">$ResMatchCount</span>/<span class="i">$ResCount</span><span class="s">)</span> <span class="co">:</span> <span class="n">0.0</span><span class="sc">;</span> | |
| 124 111 <span class="i">$PercentIdentity</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.${Precision}f"</span><span class="cm">,</span> <span class="s">(</span><span class="i">$Identity</span> * <span class="n">100</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 125 112 | |
| 126 113 <span class="k">return</span> <span class="i">$PercentIdentity</span><span class="sc">;</span> | |
| 127 114 <span class="s">}</span> | |
| 128 115 | |
| 129 116 <span class="c"># Calculate pairwise identify matrix for all the sequences and return a reference</span> | |
| 130 117 <span class="c"># to a hash with the following keys:</span> | |
| 131 118 <span class="c">#</span> | |
| 132 119 <span class="c"># {IDs} - Sequence IDs</span> | |
| 133 120 <span class="c"># {Count} - Number of IDs</span> | |
| 134 121 <span class="c"># {PercentIdentity}{$RowID}{$ColID} - Percent identify for a pair of sequences</span> | |
| 135 122 <span class="c">#</span> | |
| 136 <a name="CalculatePercentSequenceIdentityMatrix-"></a> 123 <span class="k">sub </span><span class="m">CalculatePercentSequenceIdentityMatrix</span> <span class="s">{</span> | |
| 137 124 <span class="k">my</span><span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="cm">,</span> <span class="cm">,</span> <span class="i">$Precision</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$RowID</span><span class="cm">,</span> <span class="i">$ColID</span><span class="cm">,</span> <span class="i">$RowIDSeq</span><span class="cm">,</span> <span class="i">$ColIDSeq</span><span class="cm">,</span> <span class="i">$PercentIdentity</span><span class="cm">,</span> <span class="i">%IdentityMatrixData</span><span class="s">)</span><span class="sc">;</span> | |
| 138 125 | |
| 139 126 <span class="i">$IgnoreGaps</span> = <span class="n">1</span><span class="sc">;</span> | |
| 140 127 <span class="i">$Precision</span> = <span class="n">1</span><span class="sc">;</span> | |
| 141 128 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> | |
| 142 129 <span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 143 130 <span class="s">}</span> | |
| 144 131 <span class="k">elsif</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 145 132 <span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 146 133 <span class="s">}</span> | |
| 147 134 <span class="k">else</span> <span class="s">{</span> | |
| 148 135 <span class="s">(</span><span class="i">$SequencesDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 149 136 <span class="s">}</span> | |
| 150 137 | |
| 151 138 <span class="i">%IdentityMatrixData</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 152 139 <span class="i">@</span>{<span class="i">$IdentityMatrixData</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 153 140 <span class="i">%</span>{<span class="i">$IdentityMatrixData</span>{<span class="w">PercentIdentity</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 154 141 <span class="i">$IdentityMatrixData</span>{<span class="w">Count</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 155 142 | |
| 156 143 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequencesDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 157 144 <span class="k">push</span> <span class="i">@</span>{<span class="i">$IdentityMatrixData</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> | |
| 158 145 <span class="i">$IdentityMatrixData</span>{<span class="w">Count</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 159 146 <span class="s">}</span> | |
| 160 147 <span class="c"># Initialize and calculate percent identity data values...</span> | |
| 161 148 <span class="k">for</span> <span class="i">$RowID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequencesDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 162 149 <span class="i">%</span>{<span class="i">$IdentityMatrixData</span>{<span class="w">PercentIdentity</span>}{<span class="i">$RowID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 163 150 <span class="i">$RowIDSeq</span> = <span class="i">$SequencesDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$RowID</span>}<span class="sc">;</span> | |
| 164 151 <span class="k">for</span> <span class="i">$ColID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequencesDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 165 152 <span class="i">$IdentityMatrixData</span>{<span class="i">$RowID</span>}{<span class="i">$ColID</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 166 153 <span class="i">$ColIDSeq</span> = <span class="i">$SequencesDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ColID</span>}<span class="sc">;</span> | |
| 167 154 <span class="i">$PercentIdentity</span> = <span class="i">CalcuatePercentSequenceIdentity</span><span class="s">(</span><span class="i">$RowIDSeq</span><span class="cm">,</span> <span class="i">$ColIDSeq</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span><span class="sc">;</span> | |
| 168 155 <span class="i">$IdentityMatrixData</span>{<span class="w">PercentIdentity</span>}{<span class="i">$RowID</span>}{<span class="i">$ColID</span>} = <span class="i">$PercentIdentity</span><span class="sc">;</span> | |
| 169 156 <span class="s">}</span> | |
| 170 157 <span class="s">}</span> | |
| 171 158 <span class="k">return</span> \<span class="i">%IdentityMatrixData</span><span class="sc">;</span> | |
| 172 159 <span class="s">}</span> | |
| 173 160 | |
| 174 161 <span class="c"># Retrieve information about shortest sequence...</span> | |
| 175 <a name="GetShortestSequence-"></a> 162 <span class="k">sub </span><span class="m">GetShortestSequence</span> <span class="s">{</span> | |
| 176 163 <span class="k">my</span><span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span><span class="sc">;</span> | |
| 177 164 | |
| 178 165 <span class="i">$IgnoreGaps</span> = <span class="n">1</span><span class="sc">;</span> | |
| 179 166 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 180 167 <span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 181 168 <span class="s">}</span> | |
| 182 169 <span class="k">else</span> <span class="s">{</span> | |
| 183 170 <span class="s">(</span><span class="i">$SequencesDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 184 171 <span class="s">}</span> | |
| 185 172 | |
| 186 173 <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="i">_GetShortestOrLongestSequence</span><span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="q">'Shortest'</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span><span class="sc">;</span> | |
| 187 174 <span class="k">return</span> <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span><span class="sc">;</span> | |
| 188 175 <span class="s">}</span> | |
| 189 176 | |
| 190 177 <span class="c"># Retrieve information about longest sequence..</span> | |
| 191 <a name="GetLongestSequence-"></a> 178 <span class="k">sub </span><span class="m">GetLongestSequence</span> <span class="s">{</span> | |
| 192 179 <span class="k">my</span><span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span><span class="sc">;</span> | |
| 193 180 | |
| 194 181 <span class="i">$IgnoreGaps</span> = <span class="n">1</span><span class="sc">;</span> | |
| 195 182 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 196 183 <span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 197 184 <span class="s">}</span> | |
| 198 185 <span class="k">else</span> <span class="s">{</span> | |
| 199 186 <span class="s">(</span><span class="i">$SequencesDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 200 187 <span class="s">}</span> | |
| 201 188 | |
| 202 189 <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="i">_GetShortestOrLongestSequence</span><span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="q">'Longest'</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span><span class="sc">;</span> | |
| 203 190 <span class="k">return</span> <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span><span class="sc">;</span> | |
| 204 191 <span class="s">}</span> | |
| 205 192 | |
| 206 193 <span class="c"># Get sequence length...</span> | |
| 207 <a name="GetSequenceLength-"></a> 194 <span class="k">sub </span><span class="m">GetSequenceLength</span> <span class="s">{</span> | |
| 208 195 <span class="k">my</span><span class="s">(</span><span class="i">$Seq</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span><span class="sc">;</span> | |
| 209 196 | |
| 210 197 <span class="i">$SeqLen</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$IgnoreGaps</span> = <span class="n">1</span><span class="sc">;</span> | |
| 211 198 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 212 199 <span class="s">(</span><span class="i">$Seq</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 213 200 <span class="s">}</span> | |
| 214 201 <span class="k">else</span> <span class="s">{</span> | |
| 215 202 <span class="s">(</span><span class="i">$Seq</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 216 203 <span class="s">}</span> | |
| 217 204 <span class="k">if</span> <span class="s">(</span><span class="i">$IgnoreGaps</span><span class="s">)</span> <span class="s">{</span> | |
| 218 205 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Residue</span><span class="s">)</span><span class="sc">;</span> | |
| 219 206 <span class="i">$SeqLen</span> = <span class="n">0</span><span class="sc">;</span> | |
| 220 207 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$Seq</span><span class="s">)</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 221 208 <span class="i">$Residue</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Seq</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 222 209 <span class="k">if</span> <span class="s">(</span><span class="i">$Residue</span> =~ <span class="q">/[A-Z]/i</span><span class="s">)</span> <span class="s">{</span> | |
| 223 210 <span class="i">$SeqLen</span>++<span class="sc">;</span> | |
| 224 211 <span class="s">}</span> | |
| 225 212 <span class="s">}</span> | |
| 226 213 <span class="s">}</span> | |
| 227 214 <span class="k">else</span> <span class="s">{</span> | |
| 228 215 <span class="i">$SeqLen</span> = <span class="k">length</span><span class="s">(</span><span class="i">$Seq</span><span class="s">)</span><span class="sc">;</span> | |
| 229 216 <span class="s">}</span> | |
| 230 217 | |
| 231 218 <span class="k">return</span> <span class="i">$SeqLen</span><span class="sc">;</span> | |
| 232 219 <span class="s">}</span> | |
| 233 220 | |
| 234 221 <span class="c"># Is it a gap residue...</span> | |
| 235 <a name="IsGapResidue-"></a> 222 <span class="k">sub </span><span class="m">IsGapResidue</span> <span class="s">{</span> | |
| 236 223 <span class="k">my</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 237 224 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 238 225 | |
| 239 226 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$Residue</span> !~ <span class="q">/[A-Z]/i</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 240 227 | |
| 241 228 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 242 229 <span class="s">}</span> | |
| 243 230 | |
| 244 231 <span class="c"># Is it a supported sequence file?</span> | |
| 245 232 <span class="c">#</span> | |
| 246 233 <span class="c"># Supported seqence formats are:</span> | |
| 247 234 <span class="c">#</span> | |
| 248 235 <span class="c"># ALN/ClustalW .aln</span> | |
| 249 236 <span class="c"># GCG/MSF .msf</span> | |
| 250 237 <span class="c"># PILEUP/MSF .msf</span> | |
| 251 238 <span class="c"># Fasts(Pearson) .fasta, .fta</span> | |
| 252 239 <span class="c"># NBRF/PIR .pir</span> | |
| 253 240 <span class="c">#</span> | |
| 254 <a name="IsSupportedSequenceFile-"></a> 241 <span class="k">sub </span><span class="m">IsSupportedSequenceFile</span> <span class="s">{</span> | |
| 255 242 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 256 243 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$SequenceFormat</span><span class="s">)</span><span class="sc">;</span> | |
| 257 244 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$SequenceFormat</span> = <span class="q">'NotSupported'</span><span class="sc">;</span> | |
| 258 245 | |
| 259 246 <span class="j">SEQFORMAT:</span> <span class="s">{</span> | |
| 260 247 <span class="k">if</span> <span class="s">(</span><span class="i">IsClustalWSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span><span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$SequenceFormat</span> = <span class="q">'ClustalW'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SEQFORMAT</span><span class="s">}</span> | |
| 261 248 <span class="k">if</span> <span class="s">(</span><span class="i">IsPearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span><span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$SequenceFormat</span> = <span class="q">'Pearson'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SEQFORMAT</span><span class="s">}</span> | |
| 262 249 <span class="k">if</span> <span class="s">(</span><span class="i">IsPIRFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span><span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$SequenceFormat</span> = <span class="q">'PIR'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SEQFORMAT</span><span class="s">}</span> | |
| 263 250 <span class="k">if</span> <span class="s">(</span><span class="i">IsMSFSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span><span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$SequenceFormat</span> = <span class="q">'MSF'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">SEQFORMAT</span><span class="s">}</span> | |
| 264 251 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$SequenceFormat</span> = <span class="q">'NotSupported'</span><span class="sc">;</span> | |
| 265 252 <span class="s">}</span> | |
| 266 253 <span class="k">return</span> <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$SequenceFormat</span><span class="s">)</span><span class="sc">;</span> | |
| 267 254 <span class="s">}</span> | |
| 268 255 | |
| 269 256 <span class="c"># Is it a ClustalW multiple sequence sequence file...</span> | |
| 270 <a name="IsClustalWSequenceFile-"></a> 257 <span class="k">sub </span><span class="m">IsClustalWSequenceFile</span> <span class="s">{</span> | |
| 271 258 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 272 259 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 273 260 | |
| 274 261 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 275 262 | |
| 276 263 <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $SequenceFile: $!\n"</span><span class="sc">;</span> | |
| 277 264 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*SEQUENCEFILE</span><span class="s">)</span><span class="sc">;</span> | |
| 278 265 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/(ClustalW|Clustal W|Clustal)/i</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 279 266 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> | |
| 280 267 | |
| 281 268 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 282 269 <span class="s">}</span> | |
| 283 270 | |
| 284 271 <span class="c"># Is it a valid Pearson fasta sequence or alignment file?</span> | |
| 285 272 <span class="c">#</span> | |
| 286 <a name="IsPearsonFastaSequenceFile-"></a> 273 <span class="k">sub </span><span class="m">IsPearsonFastaSequenceFile</span> <span class="s">{</span> | |
| 287 274 <span class="k">my</span><span class="s">(</span><span class="i">$FastaFile</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 288 275 | |
| 289 276 <span class="s">(</span><span class="i">$FastaFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 290 277 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 291 278 | |
| 292 279 <span class="k">open</span> <span class="w">FASTAFILE</span><span class="cm">,</span> <span class="q">"$FastaFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $FastaFile: $!\n"</span><span class="sc">;</span> | |
| 293 280 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*FASTAFILE</span><span class="s">)</span><span class="sc">;</span> | |
| 294 281 | |
| 295 282 <span class="c"># First line starts with > and the fourth character is not ';'; otherwise, it's</span> | |
| 296 283 <span class="c"># PIR FASTA format.</span> | |
| 297 284 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^>/</span><span class="s">)</span> <span class="s">{</span> | |
| 298 285 <span class="k">my</span><span class="s">(</span><span class="i">$FourthChar</span><span class="s">)</span><span class="sc">;</span> | |
| 299 286 <span class="i">$FourthChar</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="n">3</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 300 287 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$FourthChar</span> !~ <span class="q">/\;/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 301 288 <span class="s">}</span> | |
| 302 289 <span class="k">close</span> <span class="w">FASTAFILE</span><span class="sc">;</span> | |
| 303 290 | |
| 304 291 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 305 292 <span class="s">}</span> | |
| 306 293 | |
| 307 294 <span class="c"># Is it a valid NBRF/PIR fasta sequence or alignment file?</span> | |
| 308 295 <span class="c">#</span> | |
| 309 <a name="IsPIRFastaSequenceFile-"></a> 296 <span class="k">sub </span><span class="m">IsPIRFastaSequenceFile</span> <span class="s">{</span> | |
| 310 297 <span class="k">my</span><span class="s">(</span><span class="i">$FastaFile</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 311 298 | |
| 312 299 <span class="s">(</span><span class="i">$FastaFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 313 300 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 314 301 | |
| 315 302 <span class="k">open</span> <span class="w">FASTAFILE</span><span class="cm">,</span> <span class="q">"$FastaFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $FastaFile: $!\n"</span><span class="sc">;</span> | |
| 316 303 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*FASTAFILE</span><span class="s">)</span><span class="sc">;</span> | |
| 317 304 | |
| 318 305 <span class="c"># First line starts with > and the fourth character is ';'; otherwise, it's</span> | |
| 319 306 <span class="c"># a Pearson FASTA format.</span> | |
| 320 307 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^>/</span><span class="s">)</span> <span class="s">{</span> | |
| 321 308 <span class="k">my</span><span class="s">(</span><span class="i">$FourthChar</span><span class="s">)</span><span class="sc">;</span> | |
| 322 309 <span class="i">$FourthChar</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="n">3</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 323 310 <span class="i">$Status</span> = <span class="s">(</span><span class="i">$FourthChar</span> =~ <span class="q">/\;/</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 324 311 <span class="s">}</span> | |
| 325 312 <span class="k">close</span> <span class="w">FASTAFILE</span><span class="sc">;</span> | |
| 326 313 | |
| 327 314 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 328 315 <span class="s">}</span> | |
| 329 316 | |
| 330 317 <span class="c"># Is it a valid MSF sequence or alignment file?</span> | |
| 331 318 <span class="c">#</span> | |
| 332 <a name="IsMSFSequenceFile-"></a> 319 <span class="k">sub </span><span class="m">IsMSFSequenceFile</span> <span class="s">{</span> | |
| 333 320 <span class="k">my</span><span class="s">(</span><span class="i">$MSFFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 334 321 | |
| 335 322 <span class="k">open</span> <span class="w">MSFFILE</span><span class="cm">,</span> <span class="q">"$MSFFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $MSFFile: $!\n"</span><span class="sc">;</span> | |
| 336 323 | |
| 337 324 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 338 325 | |
| 339 326 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> | |
| 340 327 <span class="c"># Find a line that contains MSF: keyword and ends with '..'</span> | |
| 341 328 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*MSFFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 342 329 <span class="i">$Line</span> = <span class="i">RemoveLeadingWhiteSpaces</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 343 330 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/MSF:/i</span> && <span class="i">$Line</span> =~ <span class="q">/\.\.[ ]*$/</span><span class="s">)</span> <span class="s">{</span> | |
| 344 331 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> | |
| 345 332 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 346 333 <span class="s">}</span> | |
| 347 334 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/(!!AA_MULTIPLE_ALIGNMENT|!!NA_MULTIPLE_ALIGNMENT|PILEUP)/i</span><span class="s">)</span> <span class="s">{</span> | |
| 348 335 <span class="c"># Pileup MSF...</span> | |
| 349 336 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> | |
| 350 337 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 351 338 <span class="s">}</span> | |
| 352 339 <span class="s">}</span> | |
| 353 340 <span class="k">close</span> <span class="w">MSFFILE</span><span class="sc">;</span> | |
| 354 341 | |
| 355 342 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 356 343 <span class="s">}</span> | |
| 357 344 | |
| 358 345 <span class="c"># Read sequence or sequence alignment file...</span> | |
| 359 <a name="ReadSequenceFile-"></a> 346 <span class="k">sub </span><span class="m">ReadSequenceFile</span> <span class="s">{</span> | |
| 360 347 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 361 348 | |
| 362 349 <span class="k">if</span> <span class="s">(</span><span class="i">IsPearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 363 350 <span class="k">return</span> <span class="i">ReadPearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 364 351 <span class="s">}</span> | |
| 365 352 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsPIRFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 366 353 <span class="k">return</span> <span class="i">ReadPIRFastaSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 367 354 <span class="s">}</span> | |
| 368 355 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsMSFSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 369 356 <span class="k">return</span> <span class="i">ReadMSFSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 370 357 <span class="s">}</span> | |
| 371 358 <span class="k">elsif</span> <span class="s">(</span><span class="i">IsClustalWSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 372 359 <span class="k">return</span> <span class="i">ReadClustalWSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 373 360 <span class="s">}</span> | |
| 374 361 <span class="k">else</span> <span class="s">{</span> | |
| 375 362 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 376 363 <span class="s">}</span> | |
| 377 364 <span class="s">}</span> | |
| 378 365 | |
| 379 366 <span class="c"># Read file and setup alignment data...</span> | |
| 380 <a name="ReadClustalWSequenceFile-"></a> 367 <span class="k">sub </span><span class="m">ReadClustalWSequenceFile</span> <span class="s">{</span> | |
| 381 368 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 382 369 | |
| 383 370 <span class="k">return</span> <span class="i">_ReadFileAndSetupSequencesData</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="cm">,</span> <span class="q">'ClustalW'</span><span class="s">)</span><span class="sc">;</span> | |
| 384 371 <span class="s">}</span> | |
| 385 372 | |
| 386 373 <span class="c"># Read file and setup alignment data...</span> | |
| 387 <a name="ReadPearsonFastaSequenceFile-"></a> 374 <span class="k">sub </span><span class="m">ReadPearsonFastaSequenceFile</span> <span class="s">{</span> | |
| 388 375 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 389 376 | |
| 390 377 <span class="k">return</span> <span class="i">_ReadFileAndSetupSequencesData</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="cm">,</span> <span class="q">'Pearson'</span><span class="s">)</span><span class="sc">;</span> | |
| 391 378 <span class="s">}</span> | |
| 392 379 | |
| 393 380 <span class="c"># Read file and setup alignment data...</span> | |
| 394 <a name="ReadPIRFastaSequenceFile-"></a> 381 <span class="k">sub </span><span class="m">ReadPIRFastaSequenceFile</span> <span class="s">{</span> | |
| 395 382 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 396 383 | |
| 397 384 <span class="k">return</span> <span class="i">_ReadFileAndSetupSequencesData</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="cm">,</span> <span class="q">'PIR'</span><span class="s">)</span><span class="sc">;</span> | |
| 398 385 <span class="s">}</span> | |
| 399 386 | |
| 400 387 | |
| 401 388 <span class="c"># Read file and setup sequence data...</span> | |
| 402 <a name="ReadMSFSequenceFile-"></a> 389 <span class="k">sub </span><span class="m">ReadMSFSequenceFile</span> <span class="s">{</span> | |
| 403 390 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 404 391 | |
| 405 392 <span class="k">return</span> <span class="i">_ReadFileAndSetupSequencesData</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="cm">,</span> <span class="q">'MSF'</span><span class="s">)</span><span class="sc">;</span> | |
| 406 393 <span class="s">}</span> | |
| 407 394 | |
| 408 395 <span class="c"># Write out a Pearson FASTA file...</span> | |
| 409 <a name="WritePearsonFastaSequenceFile-"></a> 396 <span class="k">sub </span><span class="m">WritePearsonFastaSequenceFile</span> <span class="s">{</span> | |
| 410 397 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$MaxLength</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Description</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$WrappedSequence</span><span class="s">)</span><span class="sc">;</span> | |
| 411 398 | |
| 412 399 <span class="i">$MaxLength</span> = <span class="n">80</span><span class="sc">;</span> | |
| 413 400 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> | |
| 414 401 <span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$MaxLength</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 415 402 <span class="s">}</span> | |
| 416 403 <span class="k">elsif</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 417 404 <span class="s">(</span><span class="i">$SequenceFileName</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 418 405 <span class="s">}</span> | |
| 419 406 <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">">$SequenceFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Can't open $SequenceFileName: $!\n"</span><span class="sc">;</span> | |
| 420 407 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 421 408 <span class="i">$Description</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span> | |
| 422 409 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> | |
| 423 410 <span class="i">$WrappedSequence</span> = <span class="i">WrapText</span><span class="s">(</span><span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$MaxLength</span><span class="cm">,</span> <span class="q">"\n"</span><span class="s">)</span><span class="sc">;</span> | |
| 424 411 | |
| 425 412 <span class="c"># Description also contains ID...</span> | |
| 426 413 <span class="k">print</span> <span class="i">SEQUENCEFILE</span> <span class="q">">$Description\n"</span><span class="sc">;</span> | |
| 427 414 <span class="k">print</span> <span class="i">SEQUENCEFILE</span> <span class="q">"$WrappedSequence\n"</span><span class="sc">;</span> | |
| 428 415 <span class="s">}</span> | |
| 429 416 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> | |
| 430 417 <span class="s">}</span> | |
| 431 418 | |
| 432 419 <span class="c"># Get ID, Sequence and Length for smallest or longest sequence</span> | |
| 433 <a name="_GetShortestOrLongestSequence-"></a> 420 <span class="k">sub </span><span class="m">_GetShortestOrLongestSequence</span> <span class="s">{</span> | |
| 434 421 <span class="k">my</span><span class="s">(</span><span class="i">$SequencesDataRef</span><span class="cm">,</span> <span class="i">$SequenceType</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 435 422 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Seq</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="cm">,</span> <span class="i">$FirstID</span><span class="cm">,</span> <span class="i">$FirstSeqLen</span><span class="cm">,</span> <span class="i">$CurrentID</span><span class="cm">,</span> <span class="i">$CurrentSeq</span><span class="cm">,</span> <span class="i">$CurrentSeqLen</span><span class="cm">,</span> <span class="i">$CurrentDescription</span><span class="s">)</span><span class="sc">;</span> | |
| 436 423 | |
| 437 424 <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Seq</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="s">)</span> = <span class="s">(</span><span class="q">''</span><span class="cm">,</span> <span class="q">''</span><span class="cm">,</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span> | |
| 438 425 <span class="i">$FirstID</span> = <span class="q">''</span><span class="sc">;</span> | |
| 439 426 | |
| 440 427 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$CurrentID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequencesDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 441 428 <span class="i">$CurrentSeq</span> = <span class="i">$IgnoreGaps</span> ? <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$SequencesDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$CurrentID</span>}<span class="s">)</span> <span class="co">:</span> <span class="i">$SequencesDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$CurrentID</span>}<span class="sc">;</span> | |
| 442 429 <span class="i">$CurrentSeqLen</span> = <span class="i">GetSequenceLength</span><span class="s">(</span><span class="i">$CurrentSeq</span><span class="cm">,</span> <span class="i">$IgnoreGaps</span><span class="s">)</span><span class="sc">;</span> | |
| 443 430 <span class="i">$CurrentDescription</span> = <span class="i">$SequencesDataRef</span>->{<span class="w">Description</span>}{<span class="i">$CurrentID</span>}<span class="sc">;</span> | |
| 444 431 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FirstID</span><span class="s">)</span> <span class="s">{</span> | |
| 445 432 <span class="i">$FirstID</span> = <span class="i">$ID</span><span class="sc">;</span> <span class="i">$FirstSeqLen</span> = <span class="i">$CurrentSeqLen</span><span class="sc">;</span> | |
| 446 433 <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Seq</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="s">(</span><span class="i">$CurrentID</span><span class="cm">,</span> <span class="i">$CurrentSeq</span><span class="cm">,</span> <span class="i">$CurrentSeqLen</span><span class="cm">,</span> <span class="i">$CurrentDescription</span><span class="s">)</span><span class="sc">;</span> | |
| 447 434 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> | |
| 448 435 <span class="s">}</span> | |
| 449 436 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentSeqLen</span> != <span class="i">$SeqLen</span><span class="s">)</span> <span class="s">{</span> | |
| 450 437 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$SequenceType</span> =~ <span class="q">/Shortest/i</span><span class="s">)</span> && <span class="s">(</span><span class="i">$CurrentSeqLen</span> < <span class="i">$SeqLen</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 451 438 <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Seq</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="s">(</span><span class="i">$CurrentID</span><span class="cm">,</span> <span class="i">$CurrentSeq</span><span class="cm">,</span> <span class="i">$CurrentSeqLen</span><span class="cm">,</span> <span class="i">$CurrentDescription</span><span class="s">)</span><span class="sc">;</span> | |
| 452 439 <span class="s">}</span> | |
| 453 440 <span class="k">elsif</span> <span class="s">(</span><span class="s">(</span><span class="i">$SequenceType</span> =~ <span class="q">/Longest/i</span><span class="s">)</span> && <span class="s">(</span><span class="i">$CurrentSeqLen</span> > <span class="i">$SeqLen</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 454 441 <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Seq</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="s">(</span><span class="i">$CurrentID</span><span class="cm">,</span> <span class="i">$CurrentSeq</span><span class="cm">,</span> <span class="i">$CurrentSeqLen</span><span class="cm">,</span> <span class="i">$CurrentDescription</span><span class="s">)</span><span class="sc">;</span> | |
| 455 442 <span class="s">}</span> | |
| 456 443 <span class="s">}</span> | |
| 457 444 <span class="s">}</span> | |
| 458 445 <span class="k">return</span> <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Seq</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span><span class="sc">;</span> | |
| 459 446 <span class="s">}</span> | |
| 460 447 | |
| 461 448 <span class="c"># Remove gaps in the sequence and return new sequence...</span> | |
| 462 <a name="RemoveSequenceGaps-"></a> 449 <span class="k">sub </span><span class="m">RemoveSequenceGaps</span> <span class="s">{</span> | |
| 463 450 <span class="k">my</span><span class="s">(</span><span class="i">$Seq</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 464 451 <span class="k">my</span><span class="s">(</span><span class="i">$SeqWithoutGaps</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Residue</span><span class="s">)</span><span class="sc">;</span> | |
| 465 452 | |
| 466 453 <span class="i">$SeqWithoutGaps</span> = <span class="q">''</span><span class="sc">;</span> | |
| 467 454 <span class="i">$SeqLen</span> = <span class="k">length</span><span class="s">(</span><span class="i">$Seq</span><span class="s">)</span><span class="sc">;</span> | |
| 468 455 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$SeqLen</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 469 456 <span class="i">$Residue</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Seq</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 470 457 <span class="k">if</span> <span class="s">(</span><span class="i">$Residue</span> =~ <span class="q">/[A-Z]/i</span><span class="s">)</span> <span class="s">{</span> | |
| 471 458 <span class="i">$SeqWithoutGaps</span> .= <span class="i">$Residue</span><span class="sc">;</span> | |
| 472 459 <span class="s">}</span> | |
| 473 460 <span class="s">}</span> | |
| 474 461 | |
| 475 462 <span class="k">return</span> <span class="i">$SeqWithoutGaps</span><span class="sc">;</span> | |
| 476 463 <span class="s">}</span> | |
| 477 464 | |
| 478 465 <span class="c"># Using input alignment data map ref containing following keys, generate</span> | |
| 479 466 <span class="c"># a new hash with same set of keys after residue columns containg only</span> | |
| 480 467 <span class="c"># gaps have been removed:</span> | |
| 481 468 <span class="c">#</span> | |
| 482 469 <span class="c"># {IDs} : Array of IDs in order as they appear in file</span> | |
| 483 470 <span class="c"># {Count}: ID count...</span> | |
| 484 471 <span class="c"># {Description}{$ID} : Description data...</span> | |
| 485 472 <span class="c"># {Sequence}{$ID} : Sequence data...</span> | |
| 486 473 <span class="c">#</span> | |
| 487 <a name="RemoveSequenceAlignmentGapColumns-"></a> 474 <span class="k">sub </span><span class="m">RemoveSequenceAlignmentGapColumns</span> <span class="s">{</span> | |
| 488 475 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$AlignmentDataMapRef</span><span class="cm">,</span> <span class="i">%NewAlignmentDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 489 476 | |
| 490 477 <span class="s">(</span><span class="i">$AlignmentDataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 491 478 | |
| 492 479 <span class="i">%NewAlignmentDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 493 480 <span class="i">@</span>{<span class="i">$NewAlignmentDataMap</span>{<span class="w">IDs</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 494 481 <span class="i">%</span>{<span class="i">$NewAlignmentDataMap</span>{<span class="w">Description</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 495 482 <span class="i">%</span>{<span class="i">$NewAlignmentDataMap</span>{<span class="w">Sequence</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 496 483 <span class="i">$NewAlignmentDataMap</span>{<span class="w">Count</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 497 484 | |
| 498 485 <span class="c"># Transfer ID and count information...</span> | |
| 499 486 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$AlignmentDataMapRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 500 487 <span class="k">push</span> <span class="i">@</span>{<span class="i">$NewAlignmentDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> | |
| 501 488 <span class="i">$NewAlignmentDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$AlignmentDataMapRef</span>->{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span> | |
| 502 489 <span class="i">$NewAlignmentDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 503 490 <span class="i">$NewAlignmentDataMap</span>{<span class="w">Count</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 504 491 <span class="s">}</span> | |
| 505 492 | |
| 506 493 <span class="c"># Go over residue columns and transfer the data...</span> | |
| 507 494 <span class="k">my</span><span class="s">(</span><span class="i">$FirstID</span><span class="cm">,</span> <span class="i">$FirstSeq</span><span class="cm">,</span> <span class="i">$FirstSeqLen</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Res</span><span class="cm">,</span> <span class="i">$GapColumn</span><span class="s">)</span><span class="sc">;</span> | |
| 508 495 | |
| 509 496 <span class="i">$FirstID</span> = <span class="i">$AlignmentDataMapRef</span>->{<span class="w">IDs</span>}[<span class="n">0</span>]<span class="sc">;</span> | |
| 510 497 <span class="i">$FirstSeq</span> = <span class="i">$AlignmentDataMapRef</span>->{<span class="w">Sequence</span>}{<span class="i">$FirstID</span>}<span class="sc">;</span> | |
| 511 498 <span class="i">$FirstSeqLen</span> = <span class="k">length</span><span class="s">(</span><span class="i">$FirstSeq</span><span class="s">)</span><span class="sc">;</span> | |
| 512 499 | |
| 513 500 <span class="j">RES:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$FirstSeqLen</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 514 501 <span class="c"># Is this a gap column?</span> | |
| 515 502 <span class="i">$GapColumn</span> = <span class="n">1</span><span class="sc">;</span> | |
| 516 503 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$AlignmentDataMapRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 517 504 <span class="i">$Res</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$AlignmentDataMapRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 518 505 <span class="k">if</span> <span class="s">(</span><span class="i">$Res</span> =~ <span class="q">/[A-Z]/i</span><span class="s">)</span> <span class="s">{</span> | |
| 519 506 <span class="i">$GapColumn</span> = <span class="n">0</span><span class="sc">;</span> | |
| 520 507 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span> | |
| 521 508 <span class="s">}</span> | |
| 522 509 <span class="s">}</span> | |
| 523 510 <span class="k">if</span> <span class="s">(</span><span class="i">$GapColumn</span><span class="s">)</span> <span class="s">{</span> | |
| 524 511 <span class="k">next</span> <span class="j">RES</span><span class="sc">;</span> | |
| 525 512 <span class="s">}</span> | |
| 526 513 <span class="c"># Transfer this residue...</span> | |
| 527 514 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$AlignmentDataMapRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 528 515 <span class="i">$Res</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$AlignmentDataMapRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 529 516 <span class="i">$NewAlignmentDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} .= <span class="i">$Res</span><span class="sc">;</span> | |
| 530 517 <span class="s">}</span> | |
| 531 518 <span class="s">}</span> | |
| 532 519 | |
| 533 520 <span class="k">return</span> <span class="s">(</span>\<span class="i">%NewAlignmentDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 534 521 <span class="s">}</span> | |
| 535 522 | |
| 536 523 <span class="c">#</span> | |
| 537 524 <span class="c"># Read sequences file and return a reference to hash with the following keys:</span> | |
| 538 525 <span class="c">#</span> | |
| 539 526 <span class="c"># {IDs} - Array of sequence IDs</span> | |
| 540 527 <span class="c"># {Count} - Number of sequences</span> | |
| 541 528 <span class="c"># {Description}{$ID} - Sequence description</span> | |
| 542 529 <span class="c"># {Sequence}{$ID} - Sequence for a specific ID</span> | |
| 543 530 <span class="c"># {InputFileType} - Sequence file format</span> | |
| 544 531 <span class="c"># {ConservedAnnotation} - Conserved residue annonation</span> | |
| 545 532 <span class="c">#</span> | |
| 546 533 <span class="c"># Note:</span> | |
| 547 534 <span class="c"># . Conserved residue annotation either exist in the input sequence alignment file or set</span> | |
| 548 535 <span class="c"># for a file containing same number of residues for all the sequence using the following</span> | |
| 549 536 <span class="c"># notation: * - Residue conserved; ' ' - Residue not conserved.</span> | |
| 550 537 <span class="c">#</span> | |
| 551 <a name="_ReadFileAndSetupSequencesData-"></a> 538 <span class="k">sub </span><span class="m">_ReadFileAndSetupSequencesData</span> <span class="s">{</span> | |
| 552 539 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$SequenceType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 553 540 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataMapRef</span><span class="s">)</span><span class="sc">;</span> | |
| 554 541 | |
| 555 542 <span class="i">$SequenceDataMapRef</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 556 543 | |
| 557 544 <span class="c"># Read sequence file...</span> | |
| 558 545 <span class="i">$SequenceDataMapRef</span> = <span class="q">''</span><span class="sc">;</span> | |
| 559 546 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceType</span> =~ <span class="q">/^ClustalW$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 560 547 <span class="i">$SequenceDataMapRef</span> = <span class="i">_ReadClustalWFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 561 548 <span class="s">}</span> | |
| 562 549 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SequenceType</span> =~ <span class="q">/^Pearson$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 563 550 <span class="i">$SequenceDataMapRef</span> = <span class="i">_ReadPearsonFastaFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 564 551 <span class="s">}</span> | |
| 565 552 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SequenceType</span> =~ <span class="q">/^PIR$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 566 553 <span class="i">$SequenceDataMapRef</span> = <span class="i">_ReadPIRFastaFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 567 554 <span class="s">}</span> | |
| 568 555 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SequenceType</span> =~ <span class="q">/^MSF$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 569 556 <span class="i">$SequenceDataMapRef</span> = <span class="i">_ReadMSFFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 570 557 <span class="s">}</span> | |
| 571 558 <span class="k">else</span> <span class="s">{</span> | |
| 572 559 <span class="k">return</span> <span class="i">$SequenceDataMapRef</span><span class="sc">;</span> | |
| 573 560 <span class="s">}</span> | |
| 574 561 | |
| 575 562 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SequenceDataMapRef</span>->{<span class="w">ConservedAnnotation</span>}<span class="s">)</span> <span class="s">{</span> | |
| 576 563 <span class="k">return</span> <span class="s">(</span><span class="i">$SequenceDataMapRef</span><span class="s">)</span><span class="sc">;</span> | |
| 577 564 <span class="s">}</span> | |
| 578 565 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="s">(</span><span class="i">$SequenceDataMapRef</span>->{<span class="w">Count</span>} > <span class="n">1</span><span class="s">)</span> && <span class="s">(</span><span class="i">AreSequenceLengthsIdentical</span><span class="s">(</span><span class="i">$SequenceDataMapRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 579 566 <span class="k">return</span> <span class="s">(</span><span class="i">$SequenceDataMapRef</span><span class="s">)</span><span class="sc">;</span> | |
| 580 567 <span class="s">}</span> | |
| 581 568 | |
| 582 569 <span class="c"># Use the first sequence to setup an empty ConservedAnnotation key...</span> | |
| 583 570 <span class="c"># And mark fully conserved residues...</span> | |
| 584 571 <span class="c">#</span> | |
| 585 572 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$FirstSequence</span><span class="cm">,</span> <span class="i">$FirstSeqLen</span><span class="cm">,</span> <span class="i">$Res</span><span class="cm">,</span> <span class="i">$FirstRes</span><span class="cm">,</span> <span class="i">$ResConserved</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span> | |
| 586 573 <span class="i">$ID</span> = <span class="i">$SequenceDataMapRef</span>->{<span class="w">IDs</span>}[<span class="n">0</span>]<span class="sc">;</span> | |
| 587 574 <span class="i">$FirstSequence</span> = <span class="i">$SequenceDataMapRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> | |
| 588 575 <span class="i">$FirstSeqLen</span> = <span class="k">length</span><span class="s">(</span><span class="i">$FirstSequence</span><span class="s">)</span><span class="sc">;</span> | |
| 589 576 <span class="i">$SequenceDataMapRef</span>->{<span class="w">ConservedAnnotation</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 590 577 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$FirstSeqLen</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 591 578 <span class="i">$FirstRes</span> = <span class="q">''</span><span class="sc">;</span> | |
| 592 579 <span class="i">$ResConserved</span> = <span class="n">1</span><span class="sc">;</span> | |
| 593 580 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataMapRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 594 581 <span class="i">$Sequence</span> = <span class="i">$SequenceDataMapRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> | |
| 595 582 <span class="i">$Res</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 596 583 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FirstRes</span><span class="s">)</span> <span class="s">{</span> | |
| 597 584 <span class="i">$FirstRes</span> = <span class="i">$Res</span><span class="sc">;</span> | |
| 598 585 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> | |
| 599 586 <span class="s">}</span> | |
| 600 587 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Res</span> !~ <span class="q">/[A-Z]/i</span><span class="s">)</span> || <span class="s">(</span><span class="i">$Res</span> <span class="k">ne</span> <span class="i">$FirstRes</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 601 588 <span class="i">$ResConserved</span> = <span class="n">0</span><span class="sc">;</span> | |
| 602 589 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span> | |
| 603 590 <span class="s">}</span> | |
| 604 591 <span class="s">}</span> | |
| 605 592 <span class="k">if</span> <span class="s">(</span><span class="i">$ResConserved</span><span class="s">)</span> <span class="s">{</span> | |
| 606 593 <span class="i">$SequenceDataMapRef</span>->{<span class="w">ConservedAnnotation</span>} .= <span class="q">'*'</span><span class="sc">;</span> | |
| 607 594 <span class="s">}</span> | |
| 608 595 <span class="k">else</span> <span class="s">{</span> | |
| 609 596 <span class="i">$SequenceDataMapRef</span>->{<span class="w">ConservedAnnotation</span>} .= <span class="q">' '</span><span class="sc">;</span> | |
| 610 597 <span class="s">}</span> | |
| 611 598 <span class="s">}</span> | |
| 612 599 | |
| 613 600 <span class="k">return</span> <span class="s">(</span><span class="i">$SequenceDataMapRef</span><span class="s">)</span><span class="sc">;</span> | |
| 614 601 <span class="s">}</span> | |
| 615 602 | |
| 616 603 <span class="c"># Read sequence data in ClustalW multiple sequence alignment file and</span> | |
| 617 604 <span class="c"># return a reference to hash with these keys and values:</span> | |
| 618 605 <span class="c">#</span> | |
| 619 606 <span class="c"># {IDs} - Array of sequence IDs</span> | |
| 620 607 <span class="c"># {Count} - Number of sequences</span> | |
| 621 608 <span class="c"># {Description}{$ID} - Sequence description</span> | |
| 622 609 <span class="c"># {Sequence}{$ID} - Sequence for a specific ID</span> | |
| 623 610 <span class="c"># {InputFileType} - Sequence file format</span> | |
| 624 611 <span class="c"># {ConservedAnnotation} - Conserved residue annonations: space, *, : , .</span> | |
| 625 612 <span class="c">#</span> | |
| 626 613 <span class="c">#</span> | |
| 627 614 <span class="c">#</span> | |
| 628 615 <span class="c"># And based on ClustalW/X manual, here is what the ConservedAnnonations mean:</span> | |
| 629 616 <span class="c">#</span> | |
| 630 617 <span class="c"># '*' indicates positions which have a single, fully conserved residue</span> | |
| 631 618 <span class="c">#</span> | |
| 632 619 <span class="c"># ':' indicates that one of the following 'strong' groups is fully conserved: STA</span> | |
| 633 620 <span class="c"># NEQK NHQK NDEQ QHRK MILV MILF HY FYW</span> | |
| 634 621 | |
| 635 622 <span class="c"># '.' indicates that one of the following 'weaker' groups is fully conserved:</span> | |
| 636 623 <span class="c"># CSA ATV SAG STNK STPA SGND SNDEQK NDEQHK NEQHRK FVLIM HFY</span> | |
| 637 624 <span class="c">#</span> | |
| 638 625 <span class="c"># These are all the positively scoring groups that occur in the Gonnet Pam250</span> | |
| 639 626 <span class="c"># matrix. The strong and weak groups are defined as strong score >0.5 and weak</span> | |
| 640 627 <span class="c"># score =<0.5 respectively.</span> | |
| 641 628 <span class="c">#</span> | |
| 642 <a name="_ReadClustalWFile-"></a> 629 <span class="k">sub </span><span class="m">_ReadClustalWFile</span> <span class="s">{</span> | |
| 643 630 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 644 631 <span class="k">my</span><span class="s">(</span><span class="i">%SequencesDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 645 632 | |
| 646 633 <span class="c"># Initialize data...</span> | |
| 647 634 <span class="i">%SequencesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 648 635 <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 649 636 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 650 637 <span class="i">%</span>{<span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 651 638 <span class="i">$SequencesDataMap</span>{<span class="w">Count</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 652 639 <span class="i">$SequencesDataMap</span>{<span class="w">ConservedAnnotation</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 653 640 <span class="i">$SequencesDataMap</span>{<span class="w">InputFileType</span>} = <span class="q">'ClustalW'</span><span class="sc">;</span> | |
| 654 641 | |
| 655 642 <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $SequenceFile: $!\n"</span><span class="sc">;</span> | |
| 656 643 | |
| 657 644 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$LineLength</span><span class="cm">,</span> <span class="i">$AnnotationStart</span><span class="cm">,</span> <span class="i">$AnnotationLength</span><span class="cm">,</span> <span class="i">$Annotation</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SequenceLength</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$IDIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 658 645 | |
| 659 646 <span class="c"># Ignore the header line...</span> | |
| 660 647 <span class="i">$Line</span> = <span class="q"><SEQUENCEFILE></span><span class="sc">;</span> | |
| 661 648 | |
| 662 649 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*SEQUENCEFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 663 650 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^[ \*\:\.]/</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/[A-Z]/i</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 664 651 <span class="c"># Annotation for sequences: fully conserverd, weaker or stronger group conserverd.</span> | |
| 665 652 <span class="c"># Extract it and save...</span> | |
| 666 653 <span class="i">$LineLength</span> = <span class="k">length</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 667 654 <span class="i">$AnnotationStart</span> = <span class="i">$LineLength</span> - <span class="i">$SequenceLength</span><span class="sc">;</span> | |
| 668 655 <span class="i">$AnnotationLength</span> = <span class="i">$SequenceLength</span><span class="sc">;</span> | |
| 669 656 <span class="i">$Annotation</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$AnnotationStart</span><span class="cm">,</span> <span class="i">$AnnotationLength</span><span class="s">)</span><span class="sc">;</span> | |
| 670 657 <span class="i">$SequencesDataMap</span>{<span class="w">ConservedAnnotation</span>} .= <span class="i">$Annotation</span><span class="sc">;</span> | |
| 671 658 <span class="s">}</span> | |
| 672 659 <span class="k">else</span> <span class="s">{</span> | |
| 673 660 <span class="c"># Extract ID and sequences...</span> | |
| 674 661 <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="s">)</span>= <span class="i">$Line</span> =~ <span class="q">/^[ ]*(.*?)[ ]+(.*?)[ 01-9]*$/</span><span class="sc">;</span> | |
| 675 662 <span class="i">$Sequence</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 676 663 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$ID</span> && <span class="i">$Sequence</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 677 664 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 678 665 <span class="s">}</span> | |
| 679 666 | |
| 680 667 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 681 668 <span class="c"># Append to existing alignment value...</span> | |
| 682 669 <span class="i">$SequenceLength</span> = <span class="k">length</span><span class="s">(</span><span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span> | |
| 683 670 <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} .= <span class="i">$Sequence</span><span class="sc">;</span> | |
| 684 671 <span class="s">}</span> | |
| 685 672 <span class="k">else</span> <span class="s">{</span> | |
| 686 673 <span class="c"># New alignment data...</span> | |
| 687 674 <span class="i">$SequencesDataMap</span>{<span class="w">Count</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 688 675 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequencesDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> | |
| 689 676 <span class="i">$SequencesDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$ID</span><span class="sc">;</span> | |
| 690 677 <span class="i">$SequencesDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$Sequence</span><span class="sc">;</span> | |
| 691 678 <span class="i">$SequenceLength</span> = <span class="k">length</span><span class="s">(</span><span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span> | |
| 692 679 <span class="s">}</span> | |
| 693 680 <span class="s">}</span> | |
| 694 681 <span class="s">}</span> | |
| 695 682 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> | |
| 696 683 <span class="k">return</span> <span class="s">(</span>\<span class="i">%SequencesDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 697 684 <span class="s">}</span> | |
| 698 685 | |
| 699 686 <span class="c"># Read Pearson fasta file and return a reference to hash with these keys:</span> | |
| 700 687 <span class="c">#</span> | |
| 701 688 <span class="c"># {IDs} - Array of sequence IDs</span> | |
| 702 689 <span class="c"># {Count} - Number of sequences</span> | |
| 703 690 <span class="c"># {Description}{$ID} - Sequence description</span> | |
| 704 691 <span class="c"># {Sequence}{$ID} - Sequence for a specific ID</span> | |
| 705 692 <span class="c"># {InputFileType} - Sequence file format</span> | |
| 706 693 <span class="c"># {ConservedAnnotation} - Conserved residue annonation</span> | |
| 707 694 <span class="c">#</span> | |
| 708 <a name="_ReadPearsonFastaFile-"></a> 695 <span class="k">sub </span><span class="m">_ReadPearsonFastaFile</span> <span class="s">{</span> | |
| 709 696 <span class="k">my</span><span class="s">(</span><span class="i">$FastaFileName</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Description</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$IgnoreID</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">%FastaDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 710 697 | |
| 711 698 <span class="s">(</span><span class="i">$FastaFileName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 712 699 | |
| 713 700 <span class="i">%FastaDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 714 701 <span class="i">@</span>{<span class="i">$FastaDataMap</span>{<span class="w">IDs</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 715 702 <span class="i">%</span>{<span class="i">$FastaDataMap</span>{<span class="w">Description</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 716 703 <span class="i">%</span>{<span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 717 704 <span class="i">$FastaDataMap</span>{<span class="w">Count</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 718 705 <span class="i">$FastaDataMap</span>{<span class="w">InputFileType</span>} = <span class="q">'Pearson'</span><span class="sc">;</span> | |
| 719 706 | |
| 720 707 <span class="k">open</span> <span class="w">FASTAFILE</span><span class="cm">,</span> <span class="q">"$FastaFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $FastaFileName: $!\n"</span><span class="sc">;</span> | |
| 721 708 <span class="i">$ID</span> = <span class="q">''</span><span class="sc">;</span> | |
| 722 709 <span class="i">$IgnoreID</span> = <span class="n">0</span><span class="sc">;</span> | |
| 723 710 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*FASTAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 724 711 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^\>/</span><span class="s">)</span> <span class="s">{</span> | |
| 725 712 <span class="c"># Start of a new ID...</span> | |
| 726 713 <span class="i">$Line</span> =~ <span class="q">s/^\>//</span><span class="sc">;</span> | |
| 727 714 <span class="i">$Line</span> = <span class="i">RemoveLeadingWhiteSpaces</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 728 715 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 729 716 <span class="i">@LineWords</span> = <span class="k">split</span> <span class="q">/ /</span><span class="cm">,</span> <span class="i">$Line</span><span class="sc">;</span> | |
| 730 717 | |
| 731 718 <span class="i">$ID</span> = <span class="i">$LineWords</span>[<span class="n">0</span>]<span class="sc">;</span> | |
| 732 719 <span class="i">$ID</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 733 720 <span class="i">$Description</span> = <span class="i">$Line</span><span class="sc">;</span> | |
| 734 721 | |
| 735 722 <span class="i">$IgnoreID</span> = <span class="n">0</span><span class="sc">;</span> | |
| 736 723 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 737 724 <span class="i">$IgnoreID</span> = <span class="n">1</span><span class="sc">;</span> | |
| 738 725 <span class="k">warn</span> <span class="q">"Warning: ID, $ID, in Fasta file already exists. Ignoring ID and sequence data...\n"</span><span class="sc">;</span> | |
| 739 726 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 740 727 <span class="s">}</span> | |
| 741 728 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FastaDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> | |
| 742 729 <span class="i">$FastaDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$Description</span><span class="sc">;</span> | |
| 743 730 <span class="i">$FastaDataMap</span>{<span class="w">Count</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 744 731 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 745 732 <span class="s">}</span> | |
| 746 733 <span class="k">if</span> <span class="s">(</span><span class="i">$IgnoreID</span><span class="s">)</span> <span class="s">{</span> <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> <span class="s">}</span> | |
| 747 734 | |
| 748 735 <span class="c"># Remove any spaces in the sequence...</span> | |
| 749 736 <span class="i">$Line</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 750 737 <span class="c"># Sequence data for active ID...</span> | |
| 751 738 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 752 739 <span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} .= <span class="i">$Line</span><span class="sc">;</span> | |
| 753 740 <span class="s">}</span> | |
| 754 741 <span class="k">else</span> <span class="s">{</span> | |
| 755 742 <span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$Line</span><span class="sc">;</span> | |
| 756 743 <span class="s">}</span> | |
| 757 744 <span class="s">}</span> | |
| 758 745 <span class="k">close</span> <span class="w">FASTAFILE</span><span class="sc">;</span> | |
| 759 746 <span class="k">return</span> \<span class="i">%FastaDataMap</span><span class="sc">;</span> | |
| 760 747 <span class="s">}</span> | |
| 761 748 | |
| 762 749 <span class="c"># Read PIR fasta file and return a reference to hash with these keys:</span> | |
| 763 750 <span class="c">#</span> | |
| 764 751 <span class="c"># {IDs} - Array of sequence IDs</span> | |
| 765 752 <span class="c"># {Count} - Number of sequences</span> | |
| 766 753 <span class="c"># {Description}{$ID} - Sequence description</span> | |
| 767 754 <span class="c"># {Sequence}{$ID} - Sequence for a specific ID</span> | |
| 768 755 <span class="c"># {InputFileType} - Sequence file format</span> | |
| 769 756 <span class="c"># {ConservedAnnotation} - Conserved residue annonation</span> | |
| 770 757 <span class="c">#</span> | |
| 771 758 <span class="c"># Format:</span> | |
| 772 759 <span class="c"># A sequence in PIR format consists of:</span> | |
| 773 760 <span class="c"># One line starting with</span> | |
| 774 761 <span class="c"># a ">" (greater-than) sign, followed by</span> | |
| 775 762 <span class="c"># a two-letter code describing the sequence type code (P1, F1, DL, DC, RL, RC, N3, N1 or XX), followed by</span> | |
| 776 763 <span class="c"># a semicolon, followed by</span> | |
| 777 764 <span class="c"># the sequence identification code (the database ID-code).</span> | |
| 778 765 <span class="c"># One line containing a textual description of the sequence.</span> | |
| 779 766 <span class="c"># One or more lines containing the sequence itself. The end of the</span> | |
| 780 767 <span class="c"># sequence is marked by a "*" (asterisk) character.</span> | |
| 781 768 <span class="c">#</span> | |
| 782 769 <span class="c"># A file in PIR format may comprise more than one sequence.</span> | |
| 783 770 <span class="c">#</span> | |
| 784 771 <span class="c"># The PIR format is also often referred to as the NBRF format.</span> | |
| 785 772 <span class="c">#</span> | |
| 786 773 <span class="c"># Code SequenceType</span> | |
| 787 774 <span class="c"># P1 Protein (complete)</span> | |
| 788 775 <span class="c"># F1 Protein (fragment)</span> | |
| 789 776 <span class="c"># DL DNA (linear)</span> | |
| 790 777 <span class="c"># DC DNA (circular)</span> | |
| 791 778 <span class="c"># RL RNA (linear)</span> | |
| 792 779 <span class="c"># RC RNA (circular)</span> | |
| 793 780 <span class="c"># N3 tRNA</span> | |
| 794 781 <span class="c"># N1 Other functional RNA</span> | |
| 795 782 <span class="c">#</span> | |
| 796 783 | |
| 797 <a name="_ReadPIRFastaFile-"></a> 784 <span class="k">sub </span><span class="m">_ReadPIRFastaFile</span> <span class="s">{</span> | |
| 798 785 <span class="k">my</span><span class="s">(</span><span class="i">$FastaFileName</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Description</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$SequenceTypeCode</span><span class="cm">,</span> <span class="i">$ReadingSequenceData</span><span class="cm">,</span> <span class="i">%FastaDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 799 786 | |
| 800 787 <span class="s">(</span><span class="i">$FastaFileName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 801 788 | |
| 802 789 <span class="i">%FastaDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 803 790 <span class="i">@</span>{<span class="i">$FastaDataMap</span>{<span class="w">IDs</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 804 791 <span class="i">%</span>{<span class="i">$FastaDataMap</span>{<span class="w">Description</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 805 792 <span class="i">%</span>{<span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 806 793 <span class="i">%</span>{<span class="i">$FastaDataMap</span>{<span class="w">SequenceTypeCode</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 807 794 <span class="i">$FastaDataMap</span>{<span class="w">Count</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 808 795 <span class="i">$FastaDataMap</span>{<span class="w">InputFileType</span>} = <span class="q">'PIR'</span><span class="sc">;</span> | |
| 809 796 | |
| 810 797 <span class="k">open</span> <span class="w">FASTAFILE</span><span class="cm">,</span> <span class="q">"$FastaFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $FastaFileName: $!\n"</span><span class="sc">;</span> | |
| 811 798 <span class="i">$ID</span> = <span class="q">''</span><span class="sc">;</span> | |
| 812 799 <span class="i">$ReadingSequenceData</span> = <span class="n">0</span><span class="sc">;</span> | |
| 813 800 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*FASTAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 814 801 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^\>/</span><span class="s">)</span> <span class="s">{</span> | |
| 815 802 <span class="c"># Start of a new ID...</span> | |
| 816 803 <span class="i">$Line</span> =~ <span class="q">s/^\>//</span><span class="sc">;</span> | |
| 817 804 <span class="i">$Line</span> = <span class="i">RemoveLeadingWhiteSpaces</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 818 805 <span class="s">(</span><span class="i">$SequenceTypeCode</span><span class="cm">,</span> <span class="i">$ID</span><span class="s">)</span> = <span class="q">/^\>(.*?)\;(.*?)$/</span><span class="sc">;</span> | |
| 819 806 | |
| 820 807 <span class="c"># Use next line to retrieve sequence description...</span> | |
| 821 808 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*FASTAFILE</span><span class="s">)</span><span class="sc">;</span> | |
| 822 809 <span class="i">$Line</span> = <span class="i">RemoveLeadingWhiteSpaces</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 823 810 <span class="i">$Description</span> = <span class="i">$Line</span><span class="sc">;</span> | |
| 824 811 | |
| 825 812 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 826 813 <span class="k">warn</span> <span class="q">"Warning: ID, $ID, in Fasta file already exists. Ignoring ID and sequence data...\n"</span><span class="sc">;</span> | |
| 827 814 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 828 815 <span class="s">}</span> | |
| 829 816 <span class="i">$ReadingSequenceData</span> = <span class="n">1</span><span class="sc">;</span> | |
| 830 817 <span class="k">push</span> <span class="i">@</span>{<span class="i">$FastaDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> | |
| 831 818 <span class="i">$FastaDataMap</span>{<span class="w">SequenceTypeCode</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceTypeCode</span><span class="sc">;</span> | |
| 832 819 <span class="i">$FastaDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$Description</span><span class="sc">;</span> | |
| 833 820 <span class="i">$FastaDataMap</span>{<span class="w">Count</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 834 821 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 835 822 <span class="s">}</span> | |
| 836 823 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ReadingSequenceData</span><span class="s">)</span> <span class="s">{</span> <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> <span class="s">}</span> | |
| 837 824 | |
| 838 825 <span class="c"># Remove any spaces in the sequence...</span> | |
| 839 826 <span class="i">$Line</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 840 827 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/[\*]$/</span><span class="s">)</span> <span class="s">{</span> | |
| 841 828 <span class="c"># End of sequence...</span> | |
| 842 829 <span class="i">$ReadingSequenceData</span> = <span class="n">0</span><span class="sc">;</span> | |
| 843 830 <span class="i">$Line</span> =~ <span class="q">s/[\*]$//</span><span class="sc">;</span> | |
| 844 831 <span class="s">}</span> | |
| 845 832 <span class="c"># Sequence data for active ID...</span> | |
| 846 833 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 847 834 <span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} .= <span class="i">$Line</span><span class="sc">;</span> | |
| 848 835 <span class="s">}</span> | |
| 849 836 <span class="k">else</span> <span class="s">{</span> | |
| 850 837 <span class="i">$FastaDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$Line</span><span class="sc">;</span> | |
| 851 838 <span class="s">}</span> | |
| 852 839 <span class="s">}</span> | |
| 853 840 <span class="k">close</span> <span class="w">FASTAFILE</span><span class="sc">;</span> | |
| 854 841 <span class="k">return</span> \<span class="i">%FastaDataMap</span><span class="sc">;</span> | |
| 855 842 <span class="s">}</span> | |
| 856 843 | |
| 857 844 <span class="c"># Read MSF file and return a reference to hash with these keys:</span> | |
| 858 845 <span class="c">#</span> | |
| 859 846 <span class="c"># {IDs} : Array of IDs in order as they appear in file</span> | |
| 860 847 <span class="c"># {Count}: ID count...</span> | |
| 861 848 <span class="c"># {Description}{$ID} : Description data...</span> | |
| 862 849 <span class="c"># {Sequence}{$ID} : Sequence data...</span> | |
| 863 850 <span class="c">#</span> | |
| 864 <a name="_ReadMSFFile-"></a> 851 <span class="k">sub </span><span class="m">_ReadMSFFile</span> <span class="s">{</span> | |
| 865 852 <span class="k">my</span><span class="s">(</span><span class="i">$MSFFileName</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">%MSFDataMap</span><span class="s">)</span><span class="sc">;</span> | |
| 866 853 | |
| 867 854 <span class="s">(</span><span class="i">$MSFFileName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 868 855 | |
| 869 856 <span class="i">%MSFDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 870 857 <span class="i">@</span>{<span class="i">$MSFDataMap</span>{<span class="w">IDs</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 871 858 <span class="i">%</span>{<span class="i">$MSFDataMap</span>{<span class="w">Description</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 872 859 <span class="i">%</span>{<span class="i">$MSFDataMap</span>{<span class="w">Sequence</span>}} =<span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 873 860 <span class="i">$MSFDataMap</span>{<span class="w">Count</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 874 861 <span class="i">$MSFDataMap</span>{<span class="w">InputFileType</span>} = <span class="q">'MSF'</span><span class="sc">;</span> | |
| 875 862 | |
| 876 863 <span class="k">open</span> <span class="w">MSFFILE</span><span class="cm">,</span> <span class="q">"$MSFFileName"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $MSFFileName: $!\n"</span><span class="sc">;</span> | |
| 877 864 | |
| 878 865 <span class="c"># Collect sequences and IDs...</span> | |
| 879 866 <span class="c">#</span> | |
| 880 867 <span class="c"># '//' after the name fields indicates end of header list and start of sequence data.</span> | |
| 881 868 <span class="c">#</span> | |
| 882 869 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Len</span><span class="cm">,</span> <span class="i">$Check</span><span class="cm">,</span> <span class="i">$Weight</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$NameFieldsFound</span><span class="cm">,</span> <span class="i">%MSFIDsMap</span><span class="s">)</span><span class="sc">;</span> | |
| 883 870 <span class="i">%MSFIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 884 871 <span class="i">$NameFieldsFound</span> = <span class="n">0</span><span class="sc">;</span> | |
| 885 872 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*MSFFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 886 873 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/Name:/</span><span class="s">)</span> <span class="s">{</span> | |
| 887 874 <span class="i">$NameFieldsFound</span>++<span class="sc">;</span> | |
| 888 875 <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Len</span><span class="cm">,</span> <span class="i">$Check</span><span class="cm">,</span> <span class="i">$Weight</span><span class="s">)</span> = <span class="i">$Line</span> =~ <span class="q">/^[ ]*Name:[ ]+(.*?)[ ]+Len:[ ]+(.*?)[ ]+Check:[ ]+(.*?)[ ]+Weight:[ ]+(.*?)[ ]*$/</span><span class="sc">;</span> | |
| 889 876 <span class="k">if</span> <span class="s">(</span><span class="i">$ID</span> =~ <span class="q">/ /</span><span class="s">)</span> <span class="s">{</span> | |
| 890 877 <span class="s">(</span><span class="i">$ID</span><span class="s">)</span> = <span class="i">$ID</span> =~ <span class="q">/^(.*?)[ ]+/</span> | |
| 891 878 <span class="s">}</span> | |
| 892 879 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$MSFIDsMap</span>{<span class="i">$ID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 893 880 <span class="k">warn</span> <span class="q">"Warning: ID, $ID, in MSF file already exists. Ignoring ID and sequence data...\n"</span><span class="sc">;</span> | |
| 894 881 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 895 882 <span class="s">}</span> | |
| 896 883 <span class="i">$MSFIDsMap</span>{<span class="i">$ID</span>} = <span class="i">$ID</span><span class="sc">;</span> | |
| 897 884 <span class="k">push</span> <span class="i">@</span>{<span class="i">$MSFDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> | |
| 898 885 <span class="i">$MSFDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$ID</span><span class="sc">;</span> | |
| 899 886 <span class="i">$MSFDataMap</span>{<span class="w">Count</span>} += <span class="n">1</span><span class="sc">;</span> | |
| 900 887 <span class="s">}</span> | |
| 901 888 <span class="k">elsif</span> <span class="s">(</span> <span class="q">/\/\//</span> && <span class="i">$NameFieldsFound</span><span class="s">)</span> <span class="s">{</span> | |
| 902 889 <span class="c"># End of header list...</span> | |
| 903 890 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 904 891 <span class="s">}</span> | |
| 905 892 <span class="s">}</span> | |
| 906 893 <span class="c"># Collect all sequences...</span> | |
| 907 894 <span class="c">#</span> | |
| 908 895 <span class="k">my</span><span class="s">(</span><span class="i">$FirstField</span><span class="cm">,</span> <span class="i">$SecondField</span><span class="s">)</span><span class="sc">;</span> | |
| 909 896 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*MSFFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 910 897 <span class="s">(</span><span class="i">$FirstField</span><span class="cm">,</span> <span class="i">$SecondField</span><span class="s">)</span> = <span class="i">$Line</span> =~ <span class="q">/^[ ]*(.*?)[ ]+(.*?)$/</span><span class="sc">;</span> | |
| 911 898 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$MSFIDsMap</span>{<span class="i">$FirstField</span>}<span class="s">)</span> <span class="s">{</span> | |
| 912 899 <span class="c"># It's ID and sequence data...</span> | |
| 913 900 <span class="i">$ID</span> = <span class="i">$FirstField</span><span class="sc">;</span> | |
| 914 901 <span class="i">$Sequence</span> = <span class="i">$SecondField</span><span class="sc">;</span> | |
| 915 902 <span class="c"># Take out spaces and leave the gap characters...</span> | |
| 916 903 <span class="i">$Sequence</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> | |
| 917 904 <span class="k">if</span> <span class="s">(</span><span class="i">$MSFDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 918 905 <span class="i">$MSFDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} .= <span class="i">$Sequence</span><span class="sc">;</span> | |
| 919 906 <span class="s">}</span> | |
| 920 907 <span class="k">else</span> <span class="s">{</span> | |
| 921 908 <span class="i">$MSFDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$Sequence</span><span class="sc">;</span> | |
| 922 909 <span class="s">}</span> | |
| 923 910 <span class="s">}</span> | |
| 924 911 <span class="s">}</span> | |
| 925 912 | |
| 926 913 <span class="k">close</span> <span class="w">MSFFILE</span><span class="sc">;</span> | |
| 927 914 <span class="k">return</span> \<span class="i">%MSFDataMap</span><span class="sc">;</span> | |
| 928 915 <span class="s">}</span> | |
| 929 916 | |
| 930 917 | |
| 931 <a name="EOF-"></a></pre> | |
| 932 <p> </p> | |
| 933 <br /> | |
| 934 <center> | |
| 935 <img src="../../../images/h2o2.png"> | |
| 936 </center> | |
| 937 </body> | |
| 938 </html> |