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3 <title>MayaChemTools:Documentation:SequenceFileUtil.pm</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SDFileUtil.html" title="SDFileUtil.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./StatisticsUtil.html" title="StatisticsUtil.html">Next</a></td><td width="34%" align="middle"><strong>SequenceFileUtil.pm</strong></td><td width="33%" align="right"><a href="././code/SequenceFileUtil.html" title="View source code">Code</a> | <a href="./../pdf/SequenceFileUtil.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SequenceFileUtil.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SequenceFileUtil.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SequenceFileUtil.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>SequenceFileUtil</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>use SequenceFileUtil ;</p>
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26 <p>use SequenceFileUtil qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>SequenceFileUtil</strong> module provides the following functions:</p>
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31 <p> <a href="#aresequencelengthsidentical">AreSequenceLengthsIdentical</a>, <a href="#calcuatepercentsequenceidentity">CalcuatePercentSequenceIdentity</a>
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32 , <a href="#calculatepercentsequenceidentitymatrix">CalculatePercentSequenceIdentityMatrix</a>, <a href="#getlongestsequence">GetLongestSequence</a>, <a href="#getsequencelength">GetSequenceLength</a>
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33 , <a href="#getshortestsequence">GetShortestSequence</a>, <a href="#isclustalwsequencefile">IsClustalWSequenceFile</a>, <a href="#isgapresidue">IsGapResidue</a>, <a href="#ismsfsequencefile">IsMSFSequenceFile</a>
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34 , <a href="#ispirfastasequencefile">IsPIRFastaSequenceFile</a>, <a href="#ispearsonfastasequencefile">IsPearsonFastaSequenceFile</a>, <a href="#issupportedsequencefile">IsSupportedSequenceFile</a>
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35 , <a href="#readclustalwsequencefile">ReadClustalWSequenceFile</a>, <a href="#readmsfsequencefile">ReadMSFSequenceFile</a>, <a href="#readpirfastasequencefile">ReadPIRFastaSequenceFile</a>
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36 , <a href="#readpearsonfastasequencefile">ReadPearsonFastaSequenceFile</a>, <a href="#readsequencefile">ReadSequenceFile</a>, <a href="#removesequencealignmentgapcolumns">RemoveSequenceAlignmentGapColumns</a>
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37 , <a href="#removesequencegaps">RemoveSequenceGaps</a>, <a href="#writepearsonfastasequencefile">WritePearsonFastaSequenceFile</a>
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38 , <a href="#sequencefileutil module provides various methods to process sequence">SequenceFileUtil module provides various methods to process sequence</a>
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39 , <a href="#files and retreive appropriate information.">files and retreive appropriate information.</a>
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40 </p><p>
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41 </p>
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42 <h2>FUNCTIONS</h2>
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43 <dl>
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44 <dt><strong><a name="aresequencelengthsidentical" class="item"><strong>AreSequenceLengthsIdentical</strong></a></strong></dt>
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45 <dd>
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46 <div class="OptionsBox">
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47 $Status = AreSequenceLengthsIdentical($SequencesDataRef);</div>
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48 <p>Checks the lengths of all the sequences available in <em>SequencesDataRef</em> and returns 1
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49 or 0 based whether lengths of all the sequence is same.</p>
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50 </dd>
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51 <dt><strong><a name="calcuatepercentsequenceidentity" class="item"><strong>CalcuatePercentSequenceIdentity</strong></a></strong></dt>
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52 <dd>
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53 <div class="OptionsBox">
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54 $PercentIdentity =
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55 AreSequenceLengthsIdenticalAreSequenceLengthsIdentical(
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56 $Sequence1, $Sequence2, [$IgnoreGaps, $Precision]);</div>
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57 <p>Returns percent identity between <em>Sequence1</em> and <em>Sequence2</em>. Optional arguments
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58 <em>IgnoreGaps</em> and <em>Precision</em> control handling of gaps in sequences and precision of the
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59 returned value. By default, gaps are ignored and precision is set up to 1 decimal.</p>
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60 </dd>
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61 <dt><strong><a name="calculatepercentsequenceidentitymatrix" class="item"><strong>CalculatePercentSequenceIdentityMatrix</strong></a></strong></dt>
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62 <dd>
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63 <div class="OptionsBox">
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64 $IdentityMatrixDataRef = CalculatePercentSequenceIdentityMatrix(
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65 $SequencesDataRef, [$IgnoreGaps,
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66 $Precision]);</div>
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67 <p>Calculate pairwise percent identity between all the sequences available in <em>SequencesDataRef</em>
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68 and returns a reference to identity matrix hash. Optional arguments <em>IgnoreGaps</em> and
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69 <em>Precision</em> control handling of gaps in sequences and precision of the returned value. By default, gaps
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70 are ignored and precision is set up to 1 decimal.</p>
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71 </dd>
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72 <dt><strong><a name="getsequencelength" class="item"><strong>GetSequenceLength</strong></a></strong></dt>
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73 <dd>
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74 <div class="OptionsBox">
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75 $SeqquenceLength = GetSequenceLength($Sequence, [$IgnoreGaps]);</div>
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76 <p>Returns length of the specified sequence. Optional argument <em>IgnoreGaps</em> controls handling
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77 of gaps. By default, gaps are ignored.</p>
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78 </dd>
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79 <dt><strong><a name="getshortestsequence" class="item"><strong>GetShortestSequence</strong></a></strong></dt>
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80 <dd>
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81 <div class="OptionsBox">
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82 ($ID, $Sequence, $SeqLen, $Description) = GetShortestSequence(
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83 $SequencesDataRef, [$IgnoreGaps]);</div>
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84 <p>Checks the lengths of all the sequences available in $SequencesDataRef and returns $ID,
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85 $Sequence, $SeqLen, and $Description values for the shortest sequence. Optional arguments $IgnoreGaps
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86 controls handling of gaps in sequences. By default, gaps are ignored.</p>
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87 </dd>
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88 <dt><strong><a name="getlongestsequence" class="item"><strong>GetLongestSequence</strong></a></strong></dt>
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89 <dd>
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90 <div class="OptionsBox">
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91 ($ID, $Sequence, $SeqLen, $Description) = GetLongestSequence(
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92 $SequencesDataRef, [$IgnoreGaps]);</div>
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93 <p>Checks the lengths of all the sequences available in <em>SequencesDataRef</em> and returns <strong>ID</strong>,
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94 <strong>Sequence</strong>, <strong>SeqLen</strong>, and <strong>Description</strong> values for the longest sequence. Optional argument
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95 $<em>IgnoreGaps</em> controls handling of gaps in sequences. By default, gaps are ignored.</p>
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96 </dd>
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97 <dt><strong><a name="isgapresidue" class="item"><strong>IsGapResidue</strong></a></strong></dt>
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98 <dd>
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99 <div class="OptionsBox">
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100 $Status = AreSequenceLengthsIdentical($Residue);</div>
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101 <p>Returns 1 or 0 based on whether <em>Residue</em> corresponds to a gap. Any character other than A to Z is
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102 considered a gap residue.</p>
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103 </dd>
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104 <dt><strong><a name="issupportedsequencefile" class="item"><strong>IsSupportedSequenceFile</strong></a></strong></dt>
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105 <dd>
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106 <div class="OptionsBox">
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107 $Status = IsSupportedSequenceFile($SequenceFile);</div>
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108 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to a supported sequence
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109 format.</p>
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110 </dd>
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111 <dt><strong><a name="isclustalwsequencefile" class="item"><strong>IsClustalWSequenceFile</strong></a></strong></dt>
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112 <dd>
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113 <div class="OptionsBox">
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114 $Status = IsClustalWSequenceFile($SequenceFile);</div>
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115 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to Clustal sequence alignment
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116 format.</p>
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117 </dd>
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118 <dt><strong><a name="ispearsonfastasequencefile" class="item"><strong>IsPearsonFastaSequenceFile</strong></a></strong></dt>
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119 <dd>
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120 <div class="OptionsBox">
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121 $Status = IsPearsonFastaSequenceFile($SequenceFile);</div>
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122 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to Pearson FASTA sequence
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123 format.</p>
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124 </dd>
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125 <dt><strong><a name="ispirfastasequencefile" class="item"><strong>IsPIRFastaSequenceFile</strong></a></strong></dt>
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126 <dd>
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127 <div class="OptionsBox">
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128 $Status = IsPIRFastaSequenceFile($SequenceFile);</div>
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129 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to PIR FASTA sequence
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130 format.</p>
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131 </dd>
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132 <dt><strong><a name="ismsfsequencefile" class="item"><strong>IsMSFSequenceFile</strong></a></strong></dt>
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133 <dd>
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134 <div class="OptionsBox">
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135 $Status = IsClustalWSequenceFile($SequenceFile);</div>
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136 <p>Returns 1 or 0 based on whether <em>SequenceFile</em> corresponds to MSF sequence alignment
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137 format.</p>
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138 </dd>
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139 <dt><strong><a name="readsequencefile" class="item"><strong>ReadSequenceFile</strong></a></strong></dt>
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140 <dd>
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141 <div class="OptionsBox">
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142 $SequenceDataMapRef = ReadSequenceFile($SequenceFile);</div>
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143 <p>Reads <em>SequenceFile</em> and returns reference to a hash containing following key/value
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144 pairs:</p>
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145 <div class="OptionsBox">
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146 $SequenceDataMapRef->{IDs} - Array of sequence IDs
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147 <br/> $SequenceDataMapRef->{Count} - Number of sequences
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148 <br/> $SequenceDataMapRef->{Description}{$ID} - Sequence description
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149 <br/> $SequenceDataMapRef->{Sequence}{$ID} - Sequence for a specific ID
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150 <br/> $SequenceDataMapRef->{Sequence}{InputFileType} - File format</div>
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151 </dd>
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152 <dt><strong><a name="readclustalwsequencefile" class="item"><strong>ReadClustalWSequenceFile</strong></a></strong></dt>
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153 <dd>
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154 <div class="OptionsBox">
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155 $SequenceDataMapRef = ReadClustalWSequenceFile($SequenceFile);</div>
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156 <p>Reads ClustalW <em>SequenceFile</em> and returns reference to a hash containing following key/value
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157 pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
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158 </dd>
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159 <dt><strong><a name="readmsfsequencefile" class="item"><strong>ReadMSFSequenceFile</strong></a></strong></dt>
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160 <dd>
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161 <div class="OptionsBox">
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162 $SequenceDataMapRef = ReadMSFSequenceFile($SequenceFile);</div>
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163 <p>Reads MSF <em>SequenceFile</em> and returns reference to a hash containing following key/value
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164 pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
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165 </dd>
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166 <dt><strong><a name="readpirfastasequencefile" class="item"><strong>ReadPIRFastaSequenceFile</strong></a></strong></dt>
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167 <dd>
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168 <div class="OptionsBox">
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169 $SequenceDataMapRef = ReadPIRFastaSequenceFile($SequenceFile);</div>
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170 <p>Reads PIR FASTA <em>SequenceFile</em> and returns reference to a hash containing following key/value
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171 pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
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172 </dd>
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173 <dt><strong><a name="readpearsonfastasequencefile" class="item"><strong>ReadPearsonFastaSequenceFile</strong></a></strong></dt>
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174 <dd>
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175 <div class="OptionsBox">
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176 $SequenceDataMapRef = ReadPearsonFastaSequenceFile($SequenceFile);</div>
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177 <p>Reads Pearson FASTA <em>SequenceFile</em> and returns reference to a hash containing following key/value
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178 pairs as describes in <strong>ReadSequenceFile</strong> method.</p>
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179 </dd>
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180 <dt><strong><a name="removesequencegaps" class="item"><strong>RemoveSequenceGaps</strong></a></strong></dt>
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181 <dd>
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182 <div class="OptionsBox">
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183 $SeqWithoutGaps = RemoveSequenceGaps($Sequence);</div>
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184 <p>Removes gaps from <em>Sequence</em> and return a sequence without any gaps.</p>
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185 </dd>
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186 <dt><strong><a name="removesequencealignmentgapcolumns" class="item"><strong>RemoveSequenceAlignmentGapColumns</strong></a></strong></dt>
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187 <dd>
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188 <div class="OptionsBox">
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189 $NewAlignmentDataMapRef = RemoveSequenceAlignmentGapColumns(
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190 $AlignmentDataMapRef);</div>
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191 <p>Using input alignment data map ref containing following keys, generate a new hash with
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192 same set of keys after residue columns containg only gaps have been removed:</p>
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193 <div class="OptionsBox">
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194 {IDs} : Array of IDs in order as they appear in file
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195 <br/> {Count}: ID count
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196 <br/> {Description}{$ID} : Description data
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197 <br/> {Sequence}{$ID} : Sequence data</div>
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198 </dd>
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199 <dt><strong><a name="writepearsonfastasequencefile" class="item"><strong>WritePearsonFastaSequenceFile</strong></a></strong></dt>
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200 <dd>
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201 <div class="OptionsBox">
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202 WritePearsonFastaSequenceFile($SequenceFileName, $SequenceDataRef,
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203 [$MaxLength]);</div>
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204 <p>Using sequence data specified via <em>SequenceDataRef</em>, write out a Pearson FASTA sequence
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205 file. Optional argument <em>MaxLength</em> controls maximum length sequence in each line; default is
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206 80.</p>
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207 </dd>
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208 </dl>
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209 <p>
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210 </p>
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211 <h2>AUTHOR</h2>
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212 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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213 <p>
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214 </p>
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215 <h2>SEE ALSO</h2>
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216 <p><a href="./PDBFileUtil.html">PDBFileUtil.pm</a>
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217 </p>
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218 <p>
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219 </p>
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220 <h2>COPYRIGHT</h2>
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221 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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222 <p>This file is part of MayaChemTools.</p>
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223 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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224 the terms of the GNU Lesser General Public License as published by the Free
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225 Software Foundation; either version 3 of the License, or (at your option)
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226 any later version.</p>
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227 <p> </p><p> </p><div class="DocNav">
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228 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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229 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SDFileUtil.html" title="SDFileUtil.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./StatisticsUtil.html" title="StatisticsUtil.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>SequenceFileUtil.pm</strong></td></tr>
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230 </table>
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