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