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3 <title>MayaChemTools:Documentation:AnalyzeSequenceFilesData.pl</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="./AnalyzeSDFilesData.html" title="AnalyzeSDFilesData.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AnalyzeTextFilesData.html" title="AnalyzeTextFilesData.html">Next</a></td><td width="34%" align="middle"><strong>AnalyzeSequenceFilesData.pl</strong></td><td width="33%" align="right"><a href="././code/AnalyzeSequenceFilesData.html" title="View source code">Code</a> | <a href="./../pdf/AnalyzeSequenceFilesData.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/AnalyzeSequenceFilesData.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/AnalyzeSequenceFilesData.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/AnalyzeSequenceFilesData.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>AnalyzeSequenceFilesData.pl - Analyze sequence and alignment files</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>AnalyzeSequenceFilesData.pl SequenceFile(s) AlignmentFile(s)...</p>
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26 <p>AnalyzeSequenceFilesData.pl [<strong>-h, --help</strong>] [<strong>-i, --IgnoreGaps</strong> yes | no]
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27 [<strong>-m, --mode</strong> PercentIdentityMatrix | ResidueFrequencyAnalysis | All]
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28 [<strong>--outdelim</strong> comma | tab | semicolon] [<strong>-o, --overwrite</strong>] [<strong>-p, --precision</strong> number] [<strong>-q, --quote</strong> yes | no]
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29 [<strong>--ReferenceSequence</strong> SequenceID | UseFirstSequenceID]
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30 [<strong>--region</strong> "StartResNum, EndResNum, [StartResNum, EndResNum...]" | UseCompleteSequence]
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31 [<strong>--RegionResiduesMode</strong> AminoAcids | NucleicAcids | None]
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32 [<strong>-w, --WorkingDir</strong> dirname] SequenceFile(s) AlignmentFile(s)...</p>
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33 <p>
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34 </p>
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35 <h2>DESCRIPTION</h2>
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36 <p>Analyze <em>SequenceFile(s) and AlignmentFile(s)</em> data: calculate pairwise percent identity matrix or
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37 calculate percent occurrence of various residues in specified sequence regions. All the sequences
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38 in the input file must have the same sequence lengths; otherwise, the sequence file is ignored.</p>
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39 <p>The file names are separated by spaces. All the sequence files in a current directory can
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40 be specified by <em>*.aln</em>, <em>*.msf</em>, <em>*.fasta</em>, <em>*.fta</em>, <em>*.pir</em> or any other supported
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41 formats; additionally, <em>DirName</em> corresponds to all the sequence files in the current directory
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42 with any of the supported file extension: <em>.aln, .msf, .fasta, .fta, and .pir</em>.</p>
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43 <p>Supported sequence formats are: <em>ALN/CLustalW</em>, <em>GCG/MSF</em>, <em>PILEUP/MSF</em>, <em>Pearson/FASTA</em>,
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44 and <em>NBRF/PIR</em>. Instead of using file extensions, file formats are detected by parsing the contents
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45 of <em>SequenceFile(s) and AlignmentFile(s)</em>.</p>
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46 <p>
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47 </p>
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48 <h2>OPTIONS</h2>
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49 <dl>
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50 <dt><strong><strong>-h, --help</strong></strong></dt>
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51 <dd>
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52 <p>Print this help message.</p>
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53 </dd>
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54 <dt><strong><strong>-i, --IgnoreGaps</strong> <em>yes | no</em></strong></dt>
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55 <dd>
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56 <p>Ignore gaps during calculation of sequence lengths and specification of regions during residue
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57 frequency analysis. Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p>
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58 </dd>
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59 <dt><strong><strong>-m, --mode</strong> <em>PercentIdentityMatrix | ResidueFrequencyAnalysis | All</em></strong></dt>
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60 <dd>
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61 <p>Specify how to analyze data in sequence files: calculate percent identity matrix or calculate
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62 frequency of occurrence of residues in specific regions. During <em>ResidueFrequencyAnalysis</em> value
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63 of <strong>-m, --mode</strong> option, output files are generated for both the residue count and percent residue
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64 count. Possible values: <em>PercentIdentityMatrix, ResidueFrequencyAnalysis, or All</em>. Default value:
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65 <em>PercentIdentityMatrix</em>.</p>
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66 </dd>
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67 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
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68 <dd>
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69 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>.
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70 Default value: <em>comma</em>.</p>
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71 </dd>
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72 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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73 <dd>
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74 <p>Overwrite existing files.</p>
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75 </dd>
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76 <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt>
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77 <dd>
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78 <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places.
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79 Valid values: positive integers.</p>
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80 </dd>
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81 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt>
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82 <dd>
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83 <p>Put quotes around column values in output text file. Possible values: <em>yes or
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84 no</em>. Default value: <em>yes</em>.</p>
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85 </dd>
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86 <dt><strong><strong>--ReferenceSequence</strong> <em>SequenceID | UseFirstSequenceID</em></strong></dt>
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87 <dd>
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88 <p>Specify reference sequence ID to identify regions for performing <em>ResidueFrequencyAnalysis</em> specified
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89 using <strong>-m, --mode</strong> option. Default: <em>UseFirstSequenceID</em>.</p>
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90 </dd>
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91 <dt><strong><strong>--region</strong> <em>StartResNum,EndResNum,[StartResNum,EndResNum...] | UseCompleteSequence</em></strong></dt>
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92 <dd>
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93 <p>Specify how to perform frequency of occurrence analysis for residues: use specific regions
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94 indicated by starting and ending residue numbers in reference sequence or use the whole reference
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95 sequence as one region. Default: <em>UseCompleteSequence</em>.</p>
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96 <p>Based on the value of <strong>-i, --IgnoreGaps</strong> option, specified residue numbers <em>StartResNum,EndResNum</em>
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97 correspond to the positions in the reference sequence without gaps or with gaps.</p>
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98 <p>For residue numbers corresponding to the reference sequence including gaps, percent occurrence
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99 of various residues corresponding to gap position in reference sequence is also calculated.</p>
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100 </dd>
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101 <dt><strong><strong>--RegionResiduesMode</strong> <em>AminoAcids | NucleicAcids | None</em></strong></dt>
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102 <dd>
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103 <p>Specify how to process residues in the regions specified using <strong>--region</strong> option during
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104 <em>ResidueFrequencyAnalysis</em> calculation: categorize residues as amino acids, nucleic acids, or simply
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105 ignore residue category during the calculation. Possible values: <em>AminoAcids, NucleicAcids or None</em>.
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106 Default value: <em>None</em>.</p>
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107 <p>For <em>AminoAcids</em> or <em>NucleicAcids</em> values of <strong>--RegionResiduesMode</strong> option, all the standard amino
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108 acids or nucleic acids are listed in the output file for each region; Any gaps and other non standard residues
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109 are added to the list as encountered.</p>
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110 <p>For <em>None</em> value of <strong>--RegionResiduesMode</strong> option, no assumption is made about type of residues.
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111 Residue and gaps are added to the list as encountered.</p>
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112 </dd>
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113 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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114 <dd>
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115 <p>New sequence file name is generated using the root: <Root><Mode>.<Ext> and
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116 <Root><Mode><RegionNum>.<Ext>. Default new file
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117 name: <SequenceFileName><Mode>.<Ext> for <em>PercentIdentityMatrix</em> value <strong>m, --mode</strong> option
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118 and <SequenceFileName><Mode><RegionNum>.<Ext> for <em>ResidueFrequencyAnalysis</em>.
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119 The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text
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120 files respectively. This option is ignored for multiple input files.</p>
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121 </dd>
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122 <dt><strong><strong>-w --WorkingDir</strong> <em>text</em></strong></dt>
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123 <dd>
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124 <p>Location of working directory. Default: current directory.</p>
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125 </dd>
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126 </dl>
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127 <p>
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128 </p>
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129 <h2>EXAMPLES</h2>
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130 <p>To calculate percent identity matrix for all sequences in Sample1.msf file and generate
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131 Sample1PercentIdentityMatrix.csv, type:</p>
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132 <div class="ExampleBox">
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133 % AnalyzeSequenceFilesData.pl Sample1.msf</div>
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134 <p>To perform residue frequency analysis for all sequences in Sample1.aln file corresponding to
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135 non-gap positions in the first sequence and generate Sample1ResidueFrequencyAnalysisRegion1.csv
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136 and Sample1PercentResidueFrequencyAnalysisRegion1.csv files, type:</p>
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137 <div class="ExampleBox">
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138 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis -o
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139 Sample1.aln</div>
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140 <p>To perform residue frequency analysis for all sequences in Sample1.aln file corresponding to
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141 all positions in the first sequence and generate TestResidueFrequencyAnalysisRegion1.csv
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142 and TestPercentResidueFrequencyAnalysisRegion1.csv files, type:</p>
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143 <div class="ExampleBox">
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144 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis --IgnoreGaps
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145 No -o -r Test Sample1.aln</div>
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146 <p>To perform residue frequency analysis for all sequences in Sample1.aln file corresponding to
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147 non-gap residue positions 5 to 10, and 30 to 40 in sequence ACHE_BOVIN and generate
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148 Sample1ResidueFrequencyAnalysisRegion1.csv, Sample1ResidueFrequencyAnalysisRegion2.csv,
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149 SamplePercentResidueFrequencyAnalysisRegion1.csv, and
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150 SamplePercentResidueFrequencyAnalysisRegion2.csv files, type:</p>
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151 <div class="ExampleBox">
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152 % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis
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153 --ReferenceSequence ACHE_BOVIN --region "5,15,30,40" -o Sample1.msf</div>
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154 <p>
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155 </p>
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156 <h2>AUTHOR</h2>
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157 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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158 <p>
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159 </p>
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160 <h2>SEE ALSO</h2>
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161 <p><a href="./ExtractFromSequenceFiles.html">ExtractFromSequenceFiles.pl</a>, <a href="./InfoSequenceFiles.html">InfoSequenceFiles.pl</a>
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162 </p>
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163 <p>
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164 </p>
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165 <h2>COPYRIGHT</h2>
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166 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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167 <p>This file is part of MayaChemTools.</p>
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168 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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169 the terms of the GNU Lesser General Public License as published by the Free
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170 Software Foundation; either version 3 of the License, or (at your option)
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171 any later version.</p>
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172 <p> </p><p> </p><div class="DocNav">
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173 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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174 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AnalyzeSDFilesData.html" title="AnalyzeSDFilesData.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AnalyzeTextFilesData.html" title="AnalyzeTextFilesData.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>AnalyzeSequenceFilesData.pl</strong></td></tr>
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175 </table>
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176 </div>
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177 <br />
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178 <center>
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179 <img src="../../images/h2o2.png">
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