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