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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

SEE ALSO

AnalyzeSequenceFilesData.plExtractFromSequenceFiles.plInfoAminoAcids.plInfoNucleicAcids.pl

COPYRIGHT

Copyright (C) 2017 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.

 

 

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