diff docs/scripts/txt/AnalyzeSequenceFilesData.txt @ 0:4816e4a8ae95 draft default tip

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+++ b/docs/scripts/txt/AnalyzeSequenceFilesData.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    AnalyzeSequenceFilesData.pl - Analyze sequence and alignment files
+
+SYNOPSIS
+    AnalyzeSequenceFilesData.pl SequenceFile(s) AlignmentFile(s)...
+
+    AnalyzeSequenceFilesData.pl [-h, --help] [-i, --IgnoreGaps yes | no]
+    [-m, --mode PercentIdentityMatrix | ResidueFrequencyAnalysis | All]
+    [--outdelim comma | tab | semicolon] [-o, --overwrite] [-p, --precision
+    number] [-q, --quote yes | no] [--ReferenceSequence SequenceID |
+    UseFirstSequenceID] [--region "StartResNum, EndResNum, [StartResNum,
+    EndResNum...]" | UseCompleteSequence] [--RegionResiduesMode AminoAcids |
+    NucleicAcids | None] [-w, --WorkingDir dirname] SequenceFile(s)
+    AlignmentFile(s)...
+
+DESCRIPTION
+    Analyze *SequenceFile(s) and AlignmentFile(s)* data: calculate pairwise
+    percent identity matrix or calculate percent occurrence of various
+    residues in specified sequence regions. All the sequences in the input
+    file must have the same sequence lengths; otherwise, the sequence file
+    is ignored.
+
+    The file names are separated by spaces. All the sequence files in a
+    current directory can be specified by **.aln*, **.msf*, **.fasta*,
+    **.fta*, **.pir* or any other supported formats; additionally, *DirName*
+    corresponds to all the sequence files in the current directory with any
+    of the supported file extension: *.aln, .msf, .fasta, .fta, and .pir*.
+
+    Supported sequence formats are: *ALN/CLustalW*, *GCG/MSF*, *PILEUP/MSF*,
+    *Pearson/FASTA*, and *NBRF/PIR*. Instead of using file extensions, file
+    formats are detected by parsing the contents of *SequenceFile(s) and
+    AlignmentFile(s)*.
+
+OPTIONS
+    -h, --help
+        Print this help message.
+
+    -i, --IgnoreGaps *yes | no*
+        Ignore gaps during calculation of sequence lengths and specification
+        of regions during residue frequency analysis. Possible values: *yes
+        or no*. Default value: *yes*.
+
+    -m, --mode *PercentIdentityMatrix | ResidueFrequencyAnalysis | All*
+        Specify how to analyze data in sequence files: calculate percent
+        identity matrix or calculate frequency of occurrence of residues in
+        specific regions. During *ResidueFrequencyAnalysis* value of -m,
+        --mode option, output files are generated for both the residue count
+        and percent residue count. Possible values: *PercentIdentityMatrix,
+        ResidueFrequencyAnalysis, or All*. Default value:
+        *PercentIdentityMatrix*.
+
+    --outdelim *comma | tab | semicolon*
+        Output text file delimiter. Possible values: *comma, tab, or
+        semicolon*. Default value: *comma*.
+
+    -o, --overwrite
+        Overwrite existing files.
+
+    -p, --precision *number*
+        Precision of calculated values in the output file. Default: up to
+        *2* decimal places. Valid values: positive integers.
+
+    -q, --quote *yes | no*
+        Put quotes around column values in output text file. Possible
+        values: *yes or no*. Default value: *yes*.
+
+    --ReferenceSequence *SequenceID | UseFirstSequenceID*
+        Specify reference sequence ID to identify regions for performing
+        *ResidueFrequencyAnalysis* specified using -m, --mode option.
+        Default: *UseFirstSequenceID*.
+
+    --region *StartResNum,EndResNum,[StartResNum,EndResNum...] |
+    UseCompleteSequence*
+        Specify how to perform frequency of occurrence analysis for
+        residues: use specific regions indicated by starting and ending
+        residue numbers in reference sequence or use the whole reference
+        sequence as one region. Default: *UseCompleteSequence*.
+
+        Based on the value of -i, --IgnoreGaps option, specified residue
+        numbers *StartResNum,EndResNum* correspond to the positions in the
+        reference sequence without gaps or with gaps.
+
+        For residue numbers corresponding to the reference sequence
+        including gaps, percent occurrence of various residues corresponding
+        to gap position in reference sequence is also calculated.
+
+    --RegionResiduesMode *AminoAcids | NucleicAcids | None*
+        Specify how to process residues in the regions specified using
+        --region option during *ResidueFrequencyAnalysis* calculation:
+        categorize residues as amino acids, nucleic acids, or simply ignore
+        residue category during the calculation. Possible values:
+        *AminoAcids, NucleicAcids or None*. Default value: *None*.
+
+        For *AminoAcids* or *NucleicAcids* values of --RegionResiduesMode
+        option, all the standard amino acids or nucleic acids are listed in
+        the output file for each region; Any gaps and other non standard
+        residues are added to the list as encountered.
+
+        For *None* value of --RegionResiduesMode option, no assumption is
+        made about type of residues. Residue and gaps are added to the list
+        as encountered.
+
+    -r, --root *rootname*
+        New sequence file name is generated using the root:
+        <Root><Mode>.<Ext> and <Root><Mode><RegionNum>.<Ext>. Default new
+        file name: <SequenceFileName><Mode>.<Ext> for
+        *PercentIdentityMatrix* value m, --mode option and
+        <SequenceFileName><Mode><RegionNum>.<Ext> for
+        *ResidueFrequencyAnalysis*. The csv, and tsv <Ext> values are used
+        for comma/semicolon, and tab delimited text files respectively. This
+        option is ignored for multiple input files.
+
+    -w --WorkingDir *text*
+        Location of working directory. Default: current directory.
+
+EXAMPLES
+    To calculate percent identity matrix for all sequences in Sample1.msf
+    file and generate Sample1PercentIdentityMatrix.csv, type:
+
+        % AnalyzeSequenceFilesData.pl Sample1.msf
+
+    To perform residue frequency analysis for all sequences in Sample1.aln
+    file corresponding to non-gap positions in the first sequence and
+    generate Sample1ResidueFrequencyAnalysisRegion1.csv and
+    Sample1PercentResidueFrequencyAnalysisRegion1.csv files, type:
+
+        % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis -o
+          Sample1.aln
+
+    To perform residue frequency analysis for all sequences in Sample1.aln
+    file corresponding to all positions in the first sequence and generate
+    TestResidueFrequencyAnalysisRegion1.csv and
+    TestPercentResidueFrequencyAnalysisRegion1.csv files, type:
+
+        % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis --IgnoreGaps
+          No -o -r Test Sample1.aln
+
+    To perform residue frequency analysis for all sequences in Sample1.aln
+    file corresponding to non-gap residue positions 5 to 10, and 30 to 40 in
+    sequence ACHE_BOVIN and generate
+    Sample1ResidueFrequencyAnalysisRegion1.csv,
+    Sample1ResidueFrequencyAnalysisRegion2.csv,
+    SamplePercentResidueFrequencyAnalysisRegion1.csv, and
+    SamplePercentResidueFrequencyAnalysisRegion2.csv files, type:
+
+        % AnalyzeSequenceFilesData.pl -m ResidueFrequencyAnalysis
+          --ReferenceSequence ACHE_BOVIN --region "5,15,30,40" -o Sample1.msf
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    ExtractFromSequenceFiles.pl, InfoSequenceFiles.pl
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    MayaChemTools is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+