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1 NAME
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2 SequenceFileUtil
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3
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4 SYNOPSIS
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5 use SequenceFileUtil ;
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6
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7 use SequenceFileUtil qw(:all);
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8
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9 DESCRIPTION
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10 SequenceFileUtil module provides the following functions:
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11
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12 AreSequenceLengthsIdentical, CalcuatePercentSequenceIdentity,
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13 CalculatePercentSequenceIdentityMatrix, GetLongestSequence,
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14 GetSequenceLength, GetShortestSequence, IsClustalWSequenceFile,
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15 IsGapResidue, IsMSFSequenceFile, IsPIRFastaSequenceFile,
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16 IsPearsonFastaSequenceFile, IsSupportedSequenceFile,
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17 ReadClustalWSequenceFile, ReadMSFSequenceFile, ReadPIRFastaSequenceFile,
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18 ReadPearsonFastaSequenceFile, ReadSequenceFile,
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19 RemoveSequenceAlignmentGapColumns, RemoveSequenceGaps,
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20 WritePearsonFastaSequenceFile SequenceFileUtil module provides various
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21 methods to process sequence files and retreive appropriate information.
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22
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23 FUNCTIONS
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24 AreSequenceLengthsIdentical
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25 $Status = AreSequenceLengthsIdentical($SequencesDataRef);
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26
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27 Checks the lengths of all the sequences available in
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28 *SequencesDataRef* and returns 1 or 0 based whether lengths of all
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29 the sequence is same.
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30
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31 CalcuatePercentSequenceIdentity
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32 $PercentIdentity =
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33 AreSequenceLengthsIdenticalAreSequenceLengthsIdentical(
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34 $Sequence1, $Sequence2, [$IgnoreGaps, $Precision]);
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35
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36 Returns percent identity between *Sequence1* and *Sequence2*.
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37 Optional arguments *IgnoreGaps* and *Precision* control handling of
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38 gaps in sequences and precision of the returned value. By default,
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39 gaps are ignored and precision is set up to 1 decimal.
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40
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41 CalculatePercentSequenceIdentityMatrix
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42 $IdentityMatrixDataRef = CalculatePercentSequenceIdentityMatrix(
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43 $SequencesDataRef, [$IgnoreGaps,
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44 $Precision]);
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45
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46 Calculate pairwise percent identity between all the sequences
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47 available in *SequencesDataRef* and returns a reference to identity
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48 matrix hash. Optional arguments *IgnoreGaps* and *Precision* control
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49 handling of gaps in sequences and precision of the returned value.
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50 By default, gaps are ignored and precision is set up to 1 decimal.
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51
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52 GetSequenceLength
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53 $SeqquenceLength = GetSequenceLength($Sequence, [$IgnoreGaps]);
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54
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55 Returns length of the specified sequence. Optional argument
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56 *IgnoreGaps* controls handling of gaps. By default, gaps are
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57 ignored.
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58
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59 GetShortestSequence
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60 ($ID, $Sequence, $SeqLen, $Description) = GetShortestSequence(
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61 $SequencesDataRef, [$IgnoreGaps]);
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62
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63 Checks the lengths of all the sequences available in
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64 $SequencesDataRef and returns $ID, $Sequence, $SeqLen, and
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65 $Description values for the shortest sequence. Optional arguments
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66 $IgnoreGaps controls handling of gaps in sequences. By default, gaps
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67 are ignored.
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68
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69 GetLongestSequence
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70 ($ID, $Sequence, $SeqLen, $Description) = GetLongestSequence(
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71 $SequencesDataRef, [$IgnoreGaps]);
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72
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73 Checks the lengths of all the sequences available in
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74 *SequencesDataRef* and returns ID, Sequence, SeqLen, and Description
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75 values for the longest sequence. Optional argument $*IgnoreGaps*
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76 controls handling of gaps in sequences. By default, gaps are
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77 ignored.
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78
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79 IsGapResidue
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80 $Status = AreSequenceLengthsIdentical($Residue);
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81
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82 Returns 1 or 0 based on whether *Residue* corresponds to a gap. Any
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83 character other than A to Z is considered a gap residue.
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84
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85 IsSupportedSequenceFile
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86 $Status = IsSupportedSequenceFile($SequenceFile);
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87
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88 Returns 1 or 0 based on whether *SequenceFile* corresponds to a
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89 supported sequence format.
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90
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91 IsClustalWSequenceFile
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92 $Status = IsClustalWSequenceFile($SequenceFile);
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93
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94 Returns 1 or 0 based on whether *SequenceFile* corresponds to
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95 Clustal sequence alignment format.
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96
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97 IsPearsonFastaSequenceFile
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98 $Status = IsPearsonFastaSequenceFile($SequenceFile);
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99
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100 Returns 1 or 0 based on whether *SequenceFile* corresponds to
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101 Pearson FASTA sequence format.
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102
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103 IsPIRFastaSequenceFile
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104 $Status = IsPIRFastaSequenceFile($SequenceFile);
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105
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106 Returns 1 or 0 based on whether *SequenceFile* corresponds to PIR
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107 FASTA sequence format.
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108
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109 IsMSFSequenceFile
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110 $Status = IsClustalWSequenceFile($SequenceFile);
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111
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112 Returns 1 or 0 based on whether *SequenceFile* corresponds to MSF
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113 sequence alignment format.
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114
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115 ReadSequenceFile
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116 $SequenceDataMapRef = ReadSequenceFile($SequenceFile);
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117
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118 Reads *SequenceFile* and returns reference to a hash containing
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119 following key/value pairs:
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120
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121 $SequenceDataMapRef->{IDs} - Array of sequence IDs
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122 $SequenceDataMapRef->{Count} - Number of sequences
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123 $SequenceDataMapRef->{Description}{$ID} - Sequence description
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124 $SequenceDataMapRef->{Sequence}{$ID} - Sequence for a specific ID
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125 $SequenceDataMapRef->{Sequence}{InputFileType} - File format
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126
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127 ReadClustalWSequenceFile
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128 $SequenceDataMapRef = ReadClustalWSequenceFile($SequenceFile);
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129
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130 Reads ClustalW *SequenceFile* and returns reference to a hash
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131 containing following key/value pairs as describes in
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132 ReadSequenceFile method.
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133
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134 ReadMSFSequenceFile
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135 $SequenceDataMapRef = ReadMSFSequenceFile($SequenceFile);
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136
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137 Reads MSF *SequenceFile* and returns reference to a hash containing
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138 following key/value pairs as describes in ReadSequenceFile method.
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139
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140 ReadPIRFastaSequenceFile
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141 $SequenceDataMapRef = ReadPIRFastaSequenceFile($SequenceFile);
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142
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143 Reads PIR FASTA *SequenceFile* and returns reference to a hash
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144 containing following key/value pairs as describes in
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145 ReadSequenceFile method.
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146
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147 ReadPearsonFastaSequenceFile
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148 $SequenceDataMapRef = ReadPearsonFastaSequenceFile($SequenceFile);
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149
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150 Reads Pearson FASTA *SequenceFile* and returns reference to a hash
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151 containing following key/value pairs as describes in
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152 ReadSequenceFile method.
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153
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154 RemoveSequenceGaps
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155 $SeqWithoutGaps = RemoveSequenceGaps($Sequence);
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156
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157 Removes gaps from *Sequence* and return a sequence without any gaps.
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158
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159 RemoveSequenceAlignmentGapColumns
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160 $NewAlignmentDataMapRef = RemoveSequenceAlignmentGapColumns(
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161 $AlignmentDataMapRef);
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162
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163 Using input alignment data map ref containing following keys,
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164 generate a new hash with same set of keys after residue columns
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165 containg only gaps have been removed:
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166
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167 {IDs} : Array of IDs in order as they appear in file
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168 {Count}: ID count
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169 {Description}{$ID} : Description data
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170 {Sequence}{$ID} : Sequence data
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171
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172 WritePearsonFastaSequenceFile
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173 WritePearsonFastaSequenceFile($SequenceFileName, $SequenceDataRef,
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174 [$MaxLength]);
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175
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176 Using sequence data specified via *SequenceDataRef*, write out a
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177 Pearson FASTA sequence file. Optional argument *MaxLength* controls
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178 maximum length sequence in each line; default is 80.
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179
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180 AUTHOR
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181 Manish Sud <msud@san.rr.com>
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182
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183 SEE ALSO
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184 PDBFileUtil.pm
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185
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186 COPYRIGHT
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187 Copyright (C) 2015 Manish Sud. All rights reserved.
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188
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189 This file is part of MayaChemTools.
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190
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191 MayaChemTools is free software; you can redistribute it and/or modify it
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192 under the terms of the GNU Lesser General Public License as published by
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193 the Free Software Foundation; either version 3 of the License, or (at
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194 your option) any later version.
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195
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