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1 NAME
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2 AnalyzeSequenceFilesData.pl - Analyze sequence and alignment files
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3
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4 SYNOPSIS
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5 AnalyzeSequenceFilesData.pl SequenceFile(s) AlignmentFile(s)...
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6
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7 AnalyzeSequenceFilesData.pl [-h, --help] [-i, --IgnoreGaps yes | no]
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8 [-m, --mode PercentIdentityMatrix | ResidueFrequencyAnalysis | All]
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9 [--outdelim comma | tab | semicolon] [-o, --overwrite] [-p, --precision
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10 number] [-q, --quote yes | no] [--ReferenceSequence SequenceID |
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11 UseFirstSequenceID] [--region "StartResNum, EndResNum, [StartResNum,
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12 EndResNum...]" | UseCompleteSequence] [--RegionResiduesMode AminoAcids |
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13 NucleicAcids | None] [-w, --WorkingDir dirname] SequenceFile(s)
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14 AlignmentFile(s)...
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15
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16 DESCRIPTION
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17 Analyze *SequenceFile(s) and AlignmentFile(s)* data: calculate pairwise
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18 percent identity matrix or calculate percent occurrence of various
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19 residues in specified sequence regions. All the sequences in the input
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20 file must have the same sequence lengths; otherwise, the sequence file
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21 is ignored.
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22
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23 The file names are separated by spaces. All the sequence files in a
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24 current directory can be specified by **.aln*, **.msf*, **.fasta*,
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25 **.fta*, **.pir* or any other supported formats; additionally, *DirName*
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26 corresponds to all the sequence files in the current directory with any
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27 of the supported file extension: *.aln, .msf, .fasta, .fta, and .pir*.
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28
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29 Supported sequence formats are: *ALN/CLustalW*, *GCG/MSF*, *PILEUP/MSF*,
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30 *Pearson/FASTA*, and *NBRF/PIR*. Instead of using file extensions, file
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31 formats are detected by parsing the contents of *SequenceFile(s) and
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32 AlignmentFile(s)*.
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33
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34 OPTIONS
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35 -h, --help
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36 Print this help message.
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37
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38 -i, --IgnoreGaps *yes | no*
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39 Ignore gaps during calculation of sequence lengths and specification
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40 of regions during residue frequency analysis. Possible values: *yes
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41 or no*. Default value: *yes*.
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42
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43 -m, --mode *PercentIdentityMatrix | ResidueFrequencyAnalysis | All*
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44 Specify how to analyze data in sequence files: calculate percent
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45 identity matrix or calculate frequency of occurrence of residues in
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46 specific regions. During *ResidueFrequencyAnalysis* value of -m,
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47 --mode option, output files are generated for both the residue count
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48 and percent residue count. Possible values: *PercentIdentityMatrix,
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49 ResidueFrequencyAnalysis, or All*. Default value:
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50 *PercentIdentityMatrix*.
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51
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52 --outdelim *comma | tab | semicolon*
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53 Output text file delimiter. Possible values: *comma, tab, or
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54 semicolon*. Default value: *comma*.
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55
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56 -o, --overwrite
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57 Overwrite existing files.
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58
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59 -p, --precision *number*
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60 Precision of calculated values in the output file. Default: up to
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61 *2* decimal places. Valid values: positive integers.
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62
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63 -q, --quote *yes | no*
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64 Put quotes around column values in output text file. Possible
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65 values: *yes or no*. Default value: *yes*.
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66
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67 --ReferenceSequence *SequenceID | UseFirstSequenceID*
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68 Specify reference sequence ID to identify regions for performing
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69 *ResidueFrequencyAnalysis* specified using -m, --mode option.
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70 Default: *UseFirstSequenceID*.
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71
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72 --region *StartResNum,EndResNum,[StartResNum,EndResNum...] |
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73 UseCompleteSequence*
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74 Specify how to perform frequency of occurrence analysis for
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75 residues: use specific regions indicated by starting and ending
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76 residue numbers in reference sequence or use the whole reference
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77 sequence as one region. Default: *UseCompleteSequence*.
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78
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79 Based on the value of -i, --IgnoreGaps option, specified residue
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80 numbers *StartResNum,EndResNum* correspond to the positions in the
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81 reference sequence without gaps or with gaps.
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82
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83 For residue numbers corresponding to the reference sequence
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84 including gaps, percent occurrence of various residues corresponding
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85 to gap position in reference sequence is also calculated.
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86
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87 --RegionResiduesMode *AminoAcids | NucleicAcids | None*
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88 Specify how to process residues in the regions specified using
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89 --region option during *ResidueFrequencyAnalysis* calculation:
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90 categorize residues as amino acids, nucleic acids, or simply ignore
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91 residue category during the calculation. Possible values:
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92 *AminoAcids, NucleicAcids or None*. Default value: *None*.
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93
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94 For *AminoAcids* or *NucleicAcids* values of --RegionResiduesMode
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95 option, all the standard amino acids or nucleic acids are listed in
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96 the output file for each region; Any gaps and other non standard
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97 residues are added to the list as encountered.
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98
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99 For *None* value of --RegionResiduesMode option, no assumption is
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100 made about type of residues. Residue and gaps are added to the list
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101 as encountered.
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102
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103 -r, --root *rootname*
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104 New sequence file name is generated using the root:
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105 <Root><Mode>.<Ext> and <Root><Mode><RegionNum>.<Ext>. Default new
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106 file name: <SequenceFileName><Mode>.<Ext> for
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107 *PercentIdentityMatrix* value m, --mode option and
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108 <SequenceFileName><Mode><RegionNum>.<Ext> for
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109 *ResidueFrequencyAnalysis*. The csv, and tsv <Ext> values are used
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110 for comma/semicolon, and tab delimited text files respectively. This
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111 option is ignored for multiple input files.
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112
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113 -w --WorkingDir *text*
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114 Location of working directory. Default: current directory.
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115
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116 EXAMPLES
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117 To calculate percent identity matrix for all sequences in Sample1.msf
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118 file and generate Sample1PercentIdentityMatrix.csv, type:
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119
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120 % AnalyzeSequenceFilesData.pl Sample1.msf
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121
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122 To perform residue frequency analysis for all sequences in Sample1.aln
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123 file corresponding to non-gap positions in the first sequence and
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124 generate Sample1ResidueFrequencyAnalysisRegion1.csv and
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125 Sample1PercentResidueFrequencyAnalysisRegion1.csv files, type:
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126
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127 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis -o
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128 Sample1.aln
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129
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130 To perform residue frequency analysis for all sequences in Sample1.aln
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131 file corresponding to all positions in the first sequence and generate
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132 TestResidueFrequencyAnalysisRegion1.csv and
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133 TestPercentResidueFrequencyAnalysisRegion1.csv files, type:
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134
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135 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis --IgnoreGaps
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136 No -o -r Test Sample1.aln
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137
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138 To perform residue frequency analysis for all sequences in Sample1.aln
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139 file corresponding to non-gap residue positions 5 to 10, and 30 to 40 in
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140 sequence ACHE_BOVIN and generate
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141 Sample1ResidueFrequencyAnalysisRegion1.csv,
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142 Sample1ResidueFrequencyAnalysisRegion2.csv,
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143 SamplePercentResidueFrequencyAnalysisRegion1.csv, and
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144 SamplePercentResidueFrequencyAnalysisRegion2.csv files, type:
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145
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146 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis
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147 --ReferenceSequence ACHE_BOVIN --region "5,15,30,40" -o Sample1.msf
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148
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149 AUTHOR
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150 Manish Sud <msud@san.rr.com>
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151
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152 SEE ALSO
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153 ExtractFromSequenceFiles.pl, InfoSequenceFiles.pl
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154
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155 COPYRIGHT
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156 Copyright (C) 2015 Manish Sud. All rights reserved.
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157
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158 This file is part of MayaChemTools.
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159
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160 MayaChemTools is free software; you can redistribute it and/or modify it
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161 under the terms of the GNU Lesser General Public License as published by
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162 the Free Software Foundation; either version 3 of the License, or (at
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163 your option) any later version.
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164
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