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diff mayachemtools/docs/scripts/man1/AnalyzeSequenceFilesData.1 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/man1/AnalyzeSequenceFilesData.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,281 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +AnalyzeSequenceFilesData.pl \- Analyze sequence and alignment files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +AnalyzeSequenceFilesData.pl SequenceFile(s) AlignmentFile(s)... +.PP +AnalyzeSequenceFilesData.pl [\fB\-h, \-\-help\fR] [\fB\-i, \-\-IgnoreGaps\fR yes | no] +[\fB\-m, \-\-mode\fR PercentIdentityMatrix | ResidueFrequencyAnalysis | All] +[\fB\-\-outdelim\fR comma | tab | semicolon] [\fB\-o, \-\-overwrite\fR] [\fB\-p, \-\-precision\fR number] [\fB\-q, \-\-quote\fR yes | no] +[\fB\-\-ReferenceSequence\fR SequenceID | UseFirstSequenceID] +[\fB\-\-region\fR \*(L"StartResNum, EndResNum, [StartResNum, EndResNum...]\*(R" | UseCompleteSequence] +[\fB\-\-RegionResiduesMode\fR AminoAcids | NucleicAcids | None] +[\fB\-w, \-\-WorkingDir\fR dirname] SequenceFile(s) AlignmentFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Analyze \fISequenceFile(s) and AlignmentFile(s)\fR 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. +.PP +The file names are separated by spaces. All the sequence files in a current directory can +be specified by \fI*.aln\fR, \fI*.msf\fR, \fI*.fasta\fR, \fI*.fta\fR, \fI*.pir\fR or any other supported +formats; additionally, \fIDirName\fR corresponds to all the sequence files in the current directory +with any of the supported file extension: \fI.aln, .msf, .fasta, .fta, and .pir\fR. +.PP +Supported sequence formats are: \fIALN/CLustalW\fR, \fI\s-1GCG/MSF\s0\fR, \fI\s-1PILEUP/MSF\s0\fR, \fIPearson/FASTA\fR, +and \fI\s-1NBRF/PIR\s0\fR. Instead of using file extensions, file formats are detected by parsing the contents +of \fISequenceFile(s) and AlignmentFile(s)\fR. +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-i, \-\-IgnoreGaps\fR \fIyes | no\fR" 4 +.IX Item "-i, --IgnoreGaps yes | no" +Ignore gaps during calculation of sequence lengths and specification of regions during residue +frequency analysis. Possible values: \fIyes or no\fR. Default value: \fIyes\fR. +.IP "\fB\-m, \-\-mode\fR \fIPercentIdentityMatrix | ResidueFrequencyAnalysis | All\fR" 4 +.IX Item "-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 \fIResidueFrequencyAnalysis\fR value +of \fB\-m, \-\-mode\fR option, output files are generated for both the residue count and percent residue +count. Possible values: \fIPercentIdentityMatrix, ResidueFrequencyAnalysis, or All\fR. Default value: +\&\fIPercentIdentityMatrix\fR. +.IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--outdelim comma | tab | semicolon" +Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR. +Default value: \fIcomma\fR. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4 +.IX Item "-p, --precision number" +Precision of calculated values in the output file. Default: up to \fI2\fR decimal places. +Valid values: positive integers. +.IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4 +.IX Item "-q, --quote yes | no" +Put quotes around column values in output text file. Possible values: \fIyes or +no\fR. Default value: \fIyes\fR. +.IP "\fB\-\-ReferenceSequence\fR \fISequenceID | UseFirstSequenceID\fR" 4 +.IX Item "--ReferenceSequence SequenceID | UseFirstSequenceID" +Specify reference sequence \s-1ID\s0 to identify regions for performing \fIResidueFrequencyAnalysis\fR specified +using \fB\-m, \-\-mode\fR option. Default: \fIUseFirstSequenceID\fR. +.IP "\fB\-\-region\fR \fIStartResNum,EndResNum,[StartResNum,EndResNum...] | UseCompleteSequence\fR" 4 +.IX Item "--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: \fIUseCompleteSequence\fR. +.Sp +Based on the value of \fB\-i, \-\-IgnoreGaps\fR option, specified residue numbers \fIStartResNum,EndResNum\fR +correspond to the positions in the reference sequence without gaps or with gaps. +.Sp +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. +.IP "\fB\-\-RegionResiduesMode\fR \fIAminoAcids | NucleicAcids | None\fR" 4 +.IX Item "--RegionResiduesMode AminoAcids | NucleicAcids | None" +Specify how to process residues in the regions specified using \fB\-\-region\fR option during +\&\fIResidueFrequencyAnalysis\fR calculation: categorize residues as amino acids, nucleic acids, or simply +ignore residue category during the calculation. Possible values: \fIAminoAcids, NucleicAcids or None\fR. +Default value: \fINone\fR. +.Sp +For \fIAminoAcids\fR or \fINucleicAcids\fR values of \fB\-\-RegionResiduesMode\fR 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. +.Sp +For \fINone\fR value of \fB\-\-RegionResiduesMode\fR option, no assumption is made about type of residues. +Residue and gaps are added to the list as encountered. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-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 \fIPercentIdentityMatrix\fR value \fBm, \-\-mode\fR option +and <SequenceFileName><Mode><RegionNum>.<Ext> for \fIResidueFrequencyAnalysis\fR. +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. +.IP "\fB\-w \-\-WorkingDir\fR \fItext\fR" 4 +.IX Item "-w --WorkingDir text" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To calculate percent identity matrix for all sequences in Sample1.msf file and generate +Sample1PercentIdentityMatrix.csv, type: +.PP +.Vb 1 +\& % AnalyzeSequenceFilesData.pl Sample1.msf +.Ve +.PP +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: +.PP +.Vb 2 +\& % AnalyzeSequenceFilesData.pl \-m ResidueFrequencyAnalysis \-o +\& Sample1.aln +.Ve +.PP +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: +.PP +.Vb 2 +\& % AnalyzeSequenceFilesData.pl \-m ResidueFrequencyAnalysis \-\-IgnoreGaps +\& No \-o \-r Test Sample1.aln +.Ve +.PP +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 \s-1ACHE_BOVIN\s0 and generate +Sample1ResidueFrequencyAnalysisRegion1.csv, Sample1ResidueFrequencyAnalysisRegion2.csv, +SamplePercentResidueFrequencyAnalysisRegion1.csv, and +SamplePercentResidueFrequencyAnalysisRegion2.csv files, type: +.PP +.Vb 2 +\& % AnalyzeSequenceFilesData.pl \-m ResidueFrequencyAnalysis +\& \-\-ReferenceSequence ACHE_BOVIN \-\-region "5,15,30,40" \-o Sample1.msf +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +ExtractFromSequenceFiles.pl, InfoSequenceFiles.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.