view mayachemtools/docs/scripts/txt/InfoSequenceFiles.txt @ 5:9a001a14a022 draft

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NAME
    InfoSequenceFiles.pl - List information about sequence and alignment
    files

SYNOPSIS
    InfoSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...

    InfoSequenceFiles.pl [-a, --all] [-c, --count] [-d, --detail infolevel]
    [-f, --frequency] [--FrequencyBins number | "number, number,
    [number,...]"] [-h, --help] [-i, --IgnoreGaps yes | no] [-l, --longest]
    [-s, --shortest] [--SequenceLengths] [-w, --workingdir dirname]
    SequenceFile(s)...

DESCRIPTION
    List information about contents of *SequenceFile(s) and
    AlignmentFile(s)*: 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 **.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
    -a, --all
        List all the available information.

    -c, --count
        List number of of sequences. This is default behavior.

    -d, --detail *InfoLevel*
        Level of information to print about sequences during various
        options. Default: *1*. Possible values: *1, 2 or 3*.

    -f, --frequency
        List distribution of sequence lengths using the specified number of
        bins or bin range specified using FrequencyBins option.

        This option is ignored for input files containing only single
        sequence.

    --FrequencyBins *number | "number,number,[number,...]"*
        This value is used with -f, --frequency option to list distribution
        of sequence lengths using the specified number of bins or bin range.
        Default value: *10*.

        The bin range list is used to group sequence lengths into different
        groups; It must contain values in ascending order. Examples:

            100,200,300,400,500,600
            200,400,600,800,1000

        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.

    -h, --help
        Print this help message.

    -i, --IgnoreGaps *yes | no*
        Ignore gaps during calculation of sequence lengths. Possible values:
        *yes or no*. Default value: *no*.

    -l, --longest
        List information about longest sequence: ID, sequence and sequence
        length. This option is ignored for input files containing only
        single sequence.

    -s, --shortest
        List information about shortest sequence: ID, sequence and sequence
        length. This option is ignored for input files containing only
        single sequence.

    --SequenceLengths
        List information about sequence lengths.

    -w, --WorkingDir *dirname*
        Location of working directory. Default: current directory.

EXAMPLES
    To count number of sequences in sequence files, type:

        % InfoSequenceFiles.pl Sample1.fasta
        % InfoSequenceFiles.pl Sample1.msf Sample1.aln Sample1.pir
        % InfoSequenceFiles.pl *.fasta *.fta *.msf *.pir *.aln

    To list all available information with maximum level of available detail
    for a sequence alignment file Sample1.msf, type:

        % InfoSequenceFiles.pl -a -d 3 Sample1.msf

    To list sequence length information after ignoring sequence gaps in
    Sample1.aln file, type:

        % InfoSequenceFiles.pl --SequenceLengths --IgnoreGaps Yes
          Sample1.aln

    To list shortest and longest sequence length information after ignoring
    sequence gaps in Sample1.aln file, type:

        % InfoSequenceFiles.pl --longest --shortest --IgnoreGaps Yes
          Sample1.aln

    To list distribution of sequence lengths after ignoring sequence gaps in
    Sample1.aln file and report the frequency distribution into 10 bins,
    type:

        % InfoSequenceFiles.pl --frequency --FrequencyBins 10
          --IgnoreGaps Yes Sample1.aln

    To list distribution of sequence lengths after ignoring sequence gaps in
    Sample1.aln file and report the frequency distribution into specified
    bin range, type:

        % InfoSequenceFiles.pl --frequency --FrequencyBins
          "150,200,250,300,350" --IgnoreGaps Yes Sample1.aln

AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    AnalyzeSequenceFilesData.pl, ExtractFromSequenceFiles.pl,
    InfoAminoAcids.pl, InfoNucleicAcids.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.