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

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+++ b/docs/scripts/txt/ExtractFromSequenceFiles.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    ExtractFromSequenceFiles.pl - Extract data from sequence and alignment
+    files
+
+SYNOPSIS
+    ExtractFromSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...
+
+    ExtractFromSequenceFiles.pl [-h, --help] [-i, --IgnoreGaps yes | no]
+    [-m, --mode SequenceID | SequenceNum | SequenceNumRange] [-o,
+    --overwrite] [-r, --root rootname] [-s, --Sequences "SequenceID,
+    [SequenceID,...]" | "SequenceNum, [SequenceNum,...]" | "StartingSeqNum,
+    EndingSeqNum"] [--SequenceIDMatch Exact | Relaxed] [-w, --WorkingDir
+    dirname] SequenceFile(s) AlignmentFile(s)...
+
+DESCRIPTION
+    Extract specific data from *SequenceFile(s) and AlignmentFile(s)* and
+    generate FASTA files. You can extract sequences using sequence IDs or
+    sequence numbers.
+
+    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 or gap columns during during generation of new sequence
+        or alignment file(s). Possible values: *yes or no*. Default value:
+        *yes*.
+
+        In order to remove gap columns, length of all the sequence must be
+        same; otherwise, this option is ignored.
+
+    -m, --mode *SequenceID | SequenceNum | SequenceNumRange*
+        Specify how to extract data from sequence files: extract sequences
+        using sequence IDs or sequence numbers. Possible values: *SequenceID
+        | SequenceNum | SequenceNumRange*. Default: *SequenceNum* with value
+        of 1.
+
+        The sequence numbers correspond to position of sequences starting
+        from 1 for first sequence in *SequenceFile(s) and AlignmentFile(s)*.
+
+    -o, --overwrite
+        Overwrite existing files.
+
+    -r, --root *rootname*
+        New sequence file name is generated using the root:
+        <Root><Mode>.<Ext>. Default new file:
+        <SequenceFileName><Mode>.<Ext>. This option is ignored for multiple
+        input files.
+
+    -s, --Sequences *"SequenceID,[SequenceID,...]" |
+    "SequenceNum,[SequenceNum,...]" | "StartingSeqNum,EndingSeqNum"*
+        This value is -m, --mode specific. In general, it's a comma
+        delimites list of sequence IDs or sequence numbers.
+
+        For *SequenceID* value of -m, --mode option, input value format is:
+        *SequenceID,...*. Examples:
+
+            ACHE_BOVIN
+            ACHE_BOVIN,ACHE_HUMAN
+
+        For *SequenceNum* value of -m, --mode option, input value format is:
+        *SequenceNum,...*. Examples:
+
+            2
+            1,5
+
+        For *SequenceNum* value of -m, --mode option, input value format is:
+        *StaringSeqNum,EndingSeqNum*. Examples:
+
+            2,4
+
+    --SequenceIDMatch *Exact | Relaxed*
+        Sequence IDs matching criterion during *SequenceID* value of -m,
+        --mode option: match specified sequence ID exactly or as sub string
+        against sequence IDs in the files. Possible values: *Exact |
+        Relaxed*. Default: *Relaxed*. Sequence ID match is case insenstitive
+        during both options.
+
+    --SequenceLength *number*
+        Maximum sequence length per line in sequence file(s). Default: *80*.
+
+    -w --WorkingDir *text*
+        Location of working directory. Default: current directory.
+
+EXAMPLES
+    To extract first sequence from Sample1.fasta sequence file and generate
+    Sample1SequenceNum.fasta sequence file, type:
+
+        % ExtractFromSequenceFiles.pl -o Sample1.fasta
+
+    To extract first sequence from Sample1.aln alignment file and generate
+    Sample1SequenceNum.fasta sequence file without any column gaps, type:
+
+        % ExtractFromSequenceFiles.pl -o Sample1.aln
+
+    To extract first sequence from Sample1.aln alignment file and generate
+    Sample1SequenceNum.fasta sequence file with column gaps, type:
+
+        % ExtractFromSequenceFiles.pl --IgnroreGaps No -o Sample1.aln
+
+    To extract sequence number 1 and 4 from Sample1.fasta sequence file and
+    generate Sample1SequenceNum.fasta sequence file, type:
+
+        % ExtractFromSequenceFiles.pl -o -m SequenceNum --Sequences 1,4
+          -o Sample1.fasta
+
+    To extract sequences from sequence number 1 to 4 from Sample1.fasta
+    sequence file and generate Sample1SequenceNumRange.fasta sequence file,
+    type:
+
+        % ExtractFromSequenceFiles.pl -o -m SequenceNumRange --Sequences
+          1,4 -o Sample1.fasta
+
+    To extract sequence ID "Q9P993/104-387" from sequence from Sample1.fasta
+    sequence file and generate Sample1SequenceID.fasta sequence file, type:
+
+        % ExtractFromSequenceFiles.pl -o -m SequenceID --Sequences
+          "Q9P993/104-387" --SequenceIDMatch Exact -o Sample1.fasta
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    AnalyzeSequenceFilesData.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.
+