|
0
|
1 NAME
|
|
|
2 ExtractFromSequenceFiles.pl - Extract data from sequence and alignment
|
|
|
3 files
|
|
|
4
|
|
|
5 SYNOPSIS
|
|
|
6 ExtractFromSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...
|
|
|
7
|
|
|
8 ExtractFromSequenceFiles.pl [-h, --help] [-i, --IgnoreGaps yes | no]
|
|
|
9 [-m, --mode SequenceID | SequenceNum | SequenceNumRange] [-o,
|
|
|
10 --overwrite] [-r, --root rootname] [-s, --Sequences "SequenceID,
|
|
|
11 [SequenceID,...]" | "SequenceNum, [SequenceNum,...]" | "StartingSeqNum,
|
|
|
12 EndingSeqNum"] [--SequenceIDMatch Exact | Relaxed] [-w, --WorkingDir
|
|
|
13 dirname] SequenceFile(s) AlignmentFile(s)...
|
|
|
14
|
|
|
15 DESCRIPTION
|
|
|
16 Extract specific data from *SequenceFile(s) and AlignmentFile(s)* and
|
|
|
17 generate FASTA files. You can extract sequences using sequence IDs or
|
|
|
18 sequence numbers.
|
|
|
19
|
|
|
20 The file names are separated by spaces. All the sequence files in a
|
|
|
21 current directory can be specified by **.aln*, **.msf*, **.fasta*,
|
|
|
22 **.fta*, **.pir* or any other supported formats; additionally, *DirName*
|
|
|
23 corresponds to all the sequence files in the current directory with any
|
|
|
24 of the supported file extension: *.aln, .msf, .fasta, .fta, and .pir*.
|
|
|
25
|
|
|
26 Supported sequence formats are: *ALN/CLustalW*, *GCG/MSF*, *PILEUP/MSF*,
|
|
|
27 *Pearson/FASTA*, and *NBRF/PIR*. Instead of using file extensions, file
|
|
|
28 formats are detected by parsing the contents of *SequenceFile(s) and
|
|
|
29 AlignmentFile(s)*.
|
|
|
30
|
|
|
31 OPTIONS
|
|
|
32 -h, --help
|
|
|
33 Print this help message.
|
|
|
34
|
|
|
35 -i, --IgnoreGaps *yes | no*
|
|
|
36 Ignore gaps or gap columns during during generation of new sequence
|
|
|
37 or alignment file(s). Possible values: *yes or no*. Default value:
|
|
|
38 *yes*.
|
|
|
39
|
|
|
40 In order to remove gap columns, length of all the sequence must be
|
|
|
41 same; otherwise, this option is ignored.
|
|
|
42
|
|
|
43 -m, --mode *SequenceID | SequenceNum | SequenceNumRange*
|
|
|
44 Specify how to extract data from sequence files: extract sequences
|
|
|
45 using sequence IDs or sequence numbers. Possible values: *SequenceID
|
|
|
46 | SequenceNum | SequenceNumRange*. Default: *SequenceNum* with value
|
|
|
47 of 1.
|
|
|
48
|
|
|
49 The sequence numbers correspond to position of sequences starting
|
|
|
50 from 1 for first sequence in *SequenceFile(s) and AlignmentFile(s)*.
|
|
|
51
|
|
|
52 -o, --overwrite
|
|
|
53 Overwrite existing files.
|
|
|
54
|
|
|
55 -r, --root *rootname*
|
|
|
56 New sequence file name is generated using the root:
|
|
|
57 <Root><Mode>.<Ext>. Default new file:
|
|
|
58 <SequenceFileName><Mode>.<Ext>. This option is ignored for multiple
|
|
|
59 input files.
|
|
|
60
|
|
|
61 -s, --Sequences *"SequenceID,[SequenceID,...]" |
|
|
|
62 "SequenceNum,[SequenceNum,...]" | "StartingSeqNum,EndingSeqNum"*
|
|
|
63 This value is -m, --mode specific. In general, it's a comma
|
|
|
64 delimites list of sequence IDs or sequence numbers.
|
|
|
65
|
|
|
66 For *SequenceID* value of -m, --mode option, input value format is:
|
|
|
67 *SequenceID,...*. Examples:
|
|
|
68
|
|
|
69 ACHE_BOVIN
|
|
|
70 ACHE_BOVIN,ACHE_HUMAN
|
|
|
71
|
|
|
72 For *SequenceNum* value of -m, --mode option, input value format is:
|
|
|
73 *SequenceNum,...*. Examples:
|
|
|
74
|
|
|
75 2
|
|
|
76 1,5
|
|
|
77
|
|
|
78 For *SequenceNum* value of -m, --mode option, input value format is:
|
|
|
79 *StaringSeqNum,EndingSeqNum*. Examples:
|
|
|
80
|
|
|
81 2,4
|
|
|
82
|
|
|
83 --SequenceIDMatch *Exact | Relaxed*
|
|
|
84 Sequence IDs matching criterion during *SequenceID* value of -m,
|
|
|
85 --mode option: match specified sequence ID exactly or as sub string
|
|
|
86 against sequence IDs in the files. Possible values: *Exact |
|
|
|
87 Relaxed*. Default: *Relaxed*. Sequence ID match is case insenstitive
|
|
|
88 during both options.
|
|
|
89
|
|
|
90 --SequenceLength *number*
|
|
|
91 Maximum sequence length per line in sequence file(s). Default: *80*.
|
|
|
92
|
|
|
93 -w --WorkingDir *text*
|
|
|
94 Location of working directory. Default: current directory.
|
|
|
95
|
|
|
96 EXAMPLES
|
|
|
97 To extract first sequence from Sample1.fasta sequence file and generate
|
|
|
98 Sample1SequenceNum.fasta sequence file, type:
|
|
|
99
|
|
|
100 % ExtractFromSequenceFiles.pl -o Sample1.fasta
|
|
|
101
|
|
|
102 To extract first sequence from Sample1.aln alignment file and generate
|
|
|
103 Sample1SequenceNum.fasta sequence file without any column gaps, type:
|
|
|
104
|
|
|
105 % ExtractFromSequenceFiles.pl -o Sample1.aln
|
|
|
106
|
|
|
107 To extract first sequence from Sample1.aln alignment file and generate
|
|
|
108 Sample1SequenceNum.fasta sequence file with column gaps, type:
|
|
|
109
|
|
|
110 % ExtractFromSequenceFiles.pl --IgnroreGaps No -o Sample1.aln
|
|
|
111
|
|
|
112 To extract sequence number 1 and 4 from Sample1.fasta sequence file and
|
|
|
113 generate Sample1SequenceNum.fasta sequence file, type:
|
|
|
114
|
|
|
115 % ExtractFromSequenceFiles.pl -o -m SequenceNum --Sequences 1,4
|
|
|
116 -o Sample1.fasta
|
|
|
117
|
|
|
118 To extract sequences from sequence number 1 to 4 from Sample1.fasta
|
|
|
119 sequence file and generate Sample1SequenceNumRange.fasta sequence file,
|
|
|
120 type:
|
|
|
121
|
|
|
122 % ExtractFromSequenceFiles.pl -o -m SequenceNumRange --Sequences
|
|
|
123 1,4 -o Sample1.fasta
|
|
|
124
|
|
|
125 To extract sequence ID "Q9P993/104-387" from sequence from Sample1.fasta
|
|
|
126 sequence file and generate Sample1SequenceID.fasta sequence file, type:
|
|
|
127
|
|
|
128 % ExtractFromSequenceFiles.pl -o -m SequenceID --Sequences
|
|
|
129 "Q9P993/104-387" --SequenceIDMatch Exact -o Sample1.fasta
|
|
|
130
|
|
|
131 AUTHOR
|
|
|
132 Manish Sud <msud@san.rr.com>
|
|
|
133
|
|
|
134 SEE ALSO
|
|
|
135 AnalyzeSequenceFilesData.pl, InfoSequenceFiles.pl
|
|
|
136
|
|
|
137 COPYRIGHT
|
|
|
138 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
139
|
|
|
140 This file is part of MayaChemTools.
|
|
|
141
|
|
|
142 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
143 under the terms of the GNU Lesser General Public License as published by
|
|
|
144 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
145 your option) any later version.
|
|
|
146
|
