diff docs/scripts/man1/InfoSequenceFiles.1 @ 0:4816e4a8ae95 draft default tip

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+.\" ========================================================================
+.\"
+.IX Title "INFOSEQUENCEFILES 1"
+.TH INFOSEQUENCEFILES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
+.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.SH "NAME"
+InfoSequenceFiles.pl \- List information about sequence and alignment files
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+InfoSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...
+.PP
+InfoSequenceFiles.pl [\fB\-a, \-\-all\fR] [\fB\-c, \-\-count\fR] [\fB\-d, \-\-detail\fR infolevel]
+[\fB\-f, \-\-frequency\fR] [\fB\-\-FrequencyBins\fR number | \*(L"number, number, [number,...]\*(R"]
+[\fB\-h, \-\-help\fR] [\fB\-i, \-\-IgnoreGaps\fR yes | no] [\fB\-l, \-\-longest\fR] [\fB\-s, \-\-shortest\fR]
+[\fB\-\-SequenceLengths\fR] [\fB\-w, \-\-workingdir\fR dirname] SequenceFile(s)...
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+List information about contents of \fISequenceFile(s) and AlignmentFile(s)\fR: number of sequences,
+shortest and longest sequences, distribution of sequence lengths and so on. 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\-a, \-\-all\fR" 4
+.IX Item "-a, --all"
+List all the available information.
+.IP "\fB\-c, \-\-count\fR" 4
+.IX Item "-c, --count"
+List number of of sequences. This is \fBdefault behavior\fR.
+.IP "\fB\-d, \-\-detail\fR \fIInfoLevel\fR" 4
+.IX Item "-d, --detail InfoLevel"
+Level of information to print about sequences during various options. Default: \fI1\fR.
+Possible values: \fI1, 2 or 3\fR.
+.IP "\fB\-f, \-\-frequency\fR" 4
+.IX Item "-f, --frequency"
+List distribution of sequence lengths using the specified number of bins or bin range specified
+using \fBFrequencyBins\fR option.
+.Sp
+This option is ignored for input files containing only single sequence.
+.ie n .IP "\fB\-\-FrequencyBins\fR \fInumber | ""number,number,[number,...]""\fR" 4
+.el .IP "\fB\-\-FrequencyBins\fR \fInumber | ``number,number,[number,...]''\fR" 4
+.IX Item "--FrequencyBins number | number,number,[number,...]"
+This value is used with \fB\-f, \-\-frequency\fR option to list distribution of sequence lengths using
+the specified number of bins or bin range. Default value: \fI10\fR.
+.Sp
+The bin range list is used to group sequence lengths  into different groups; It must contain
+values in ascending order. Examples:
+.Sp
+.Vb 2
+\&    100,200,300,400,500,600
+\&    200,400,600,800,1000
+.Ve
+.Sp
+The frequency value calculated for a specific bin corresponds to all the sequence lengths
+which are greater than the previous bin value and less than or equal to the current bin value.
+.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. Possible values: \fIyes or
+no\fR. Default value: \fIno\fR.
+.IP "\fB\-l, \-\-longest\fR" 4
+.IX Item "-l, --longest"
+List information about longest sequence: \s-1ID\s0, sequence and sequence length. This option
+is ignored for input files containing only single sequence.
+.IP "\fB\-s, \-\-shortest\fR" 4
+.IX Item "-s, --shortest"
+List information about shortest sequence: \s-1ID\s0, sequence and sequence length. This option
+is ignored for input files containing only single sequence.
+.IP "\fB\-\-SequenceLengths\fR" 4
+.IX Item "--SequenceLengths"
+List information about sequence lengths.
+.IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4
+.IX Item "-w, --WorkingDir dirname"
+Location of working directory. Default: current directory.
+.SH "EXAMPLES"
+.IX Header "EXAMPLES"
+To count number of sequences in sequence files, type:
+.PP
+.Vb 3
+\&    % InfoSequenceFiles.pl Sample1.fasta
+\&    % InfoSequenceFiles.pl Sample1.msf Sample1.aln Sample1.pir
+\&    % InfoSequenceFiles.pl *.fasta *.fta *.msf *.pir *.aln
+.Ve
+.PP
+To list all available information with maximum level of available detail for a sequence
+alignment file Sample1.msf, type:
+.PP
+.Vb 1
+\&    % InfoSequenceFiles.pl \-a \-d 3 Sample1.msf
+.Ve
+.PP
+To list sequence length information after ignoring sequence gaps in Sample1.aln file, type:
+.PP
+.Vb 2
+\&    % InfoSequenceFiles.pl \-\-SequenceLengths \-\-IgnoreGaps Yes
+\&      Sample1.aln
+.Ve
+.PP
+To list shortest and longest sequence length information after ignoring sequence
+gaps in Sample1.aln file, type:
+.PP
+.Vb 2
+\&    % InfoSequenceFiles.pl \-\-longest \-\-shortest \-\-IgnoreGaps Yes
+\&      Sample1.aln
+.Ve
+.PP
+To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and
+report the frequency distribution into 10 bins, type:
+.PP
+.Vb 2
+\&    % InfoSequenceFiles.pl \-\-frequency \-\-FrequencyBins 10
+\&      \-\-IgnoreGaps Yes Sample1.aln
+.Ve
+.PP
+To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and
+report the frequency distribution into specified bin range, type:
+.PP
+.Vb 2
+\&    % InfoSequenceFiles.pl \-\-frequency \-\-FrequencyBins
+\&      "150,200,250,300,350" \-\-IgnoreGaps Yes Sample1.aln
+.Ve
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <[e-mail]>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+AnalyzeSequenceFilesData.pl, ExtractFromSequenceFiles.pl, InfoAminoAcids.pl, InfoNucleicAcids.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.