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1
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1 NAME
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2 InfoSequenceFiles.pl - List information about 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 InfoSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...
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7
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8 InfoSequenceFiles.pl [-a, --all] [-c, --count] [-d, --detail infolevel]
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9 [-f, --frequency] [--FrequencyBins number | "number, number,
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10 [number,...]"] [-h, --help] [-i, --IgnoreGaps yes | no] [-l, --longest]
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11 [-s, --shortest] [--SequenceLengths] [-w, --workingdir dirname]
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12 SequenceFile(s)...
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13
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14 DESCRIPTION
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15 List information about contents of *SequenceFile(s) and
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16 AlignmentFile(s)*: number of sequences, shortest and longest sequences,
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17 distribution of sequence lengths and so on. The file names are separated
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18 by spaces. All the sequence files in a current directory can be
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19 specified by **.aln*, **.msf*, **.fasta*, **.fta*, **.pir* or any other
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20 supported formats; additionally, *DirName* corresponds to all the
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21 sequence files in the current directory with any of the supported file
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22 extension: *.aln, .msf, .fasta, .fta, and .pir*.
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23
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24 Supported sequence formats are: *ALN/CLustalW*, *GCG/MSF*, *PILEUP/MSF*,
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25 *Pearson/FASTA*, and *NBRF/PIR*. Instead of using file extensions, file
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26 formats are detected by parsing the contents of *SequenceFile(s) and
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27 AlignmentFile(s)*.
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28
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29 OPTIONS
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30 -a, --all
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31 List all the available information.
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32
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33 -c, --count
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34 List number of of sequences. This is default behavior.
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35
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36 -d, --detail *InfoLevel*
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37 Level of information to print about sequences during various
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38 options. Default: *1*. Possible values: *1, 2 or 3*.
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39
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40 -f, --frequency
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41 List distribution of sequence lengths using the specified number of
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42 bins or bin range specified using FrequencyBins option.
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43
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44 This option is ignored for input files containing only single
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45 sequence.
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46
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47 --FrequencyBins *number | "number,number,[number,...]"*
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48 This value is used with -f, --frequency option to list distribution
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49 of sequence lengths using the specified number of bins or bin range.
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50 Default value: *10*.
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51
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52 The bin range list is used to group sequence lengths into different
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53 groups; It must contain values in ascending order. Examples:
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54
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55 100,200,300,400,500,600
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56 200,400,600,800,1000
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57
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58 The frequency value calculated for a specific bin corresponds to all
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59 the sequence lengths which are greater than the previous bin value
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60 and less than or equal to the current bin value.
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61
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62 -h, --help
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63 Print this help message.
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64
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65 -i, --IgnoreGaps *yes | no*
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66 Ignore gaps during calculation of sequence lengths. Possible values:
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67 *yes or no*. Default value: *no*.
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68
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69 -l, --longest
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70 List information about longest sequence: ID, sequence and sequence
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71 length. This option is ignored for input files containing only
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72 single sequence.
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73
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74 -s, --shortest
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75 List information about shortest sequence: ID, sequence and sequence
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76 length. This option is ignored for input files containing only
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77 single sequence.
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78
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79 --SequenceLengths
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80 List information about sequence lengths.
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81
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82 -w, --WorkingDir *dirname*
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83 Location of working directory. Default: current directory.
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84
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85 EXAMPLES
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86 To count number of sequences in sequence files, type:
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87
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88 % InfoSequenceFiles.pl Sample1.fasta
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89 % InfoSequenceFiles.pl Sample1.msf Sample1.aln Sample1.pir
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90 % InfoSequenceFiles.pl *.fasta *.fta *.msf *.pir *.aln
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91
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92 To list all available information with maximum level of available detail
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93 for a sequence alignment file Sample1.msf, type:
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94
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95 % InfoSequenceFiles.pl -a -d 3 Sample1.msf
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96
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97 To list sequence length information after ignoring sequence gaps in
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98 Sample1.aln file, type:
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99
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100 % InfoSequenceFiles.pl --SequenceLengths --IgnoreGaps Yes
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101 Sample1.aln
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102
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103 To list shortest and longest sequence length information after ignoring
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104 sequence gaps in Sample1.aln file, type:
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105
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106 % InfoSequenceFiles.pl --longest --shortest --IgnoreGaps Yes
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107 Sample1.aln
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108
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109 To list distribution of sequence lengths after ignoring sequence gaps in
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110 Sample1.aln file and report the frequency distribution into 10 bins,
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111 type:
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112
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113 % InfoSequenceFiles.pl --frequency --FrequencyBins 10
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114 --IgnoreGaps Yes Sample1.aln
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115
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116 To list distribution of sequence lengths after ignoring sequence gaps in
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117 Sample1.aln file and report the frequency distribution into specified
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118 bin range, type:
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119
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120 % InfoSequenceFiles.pl --frequency --FrequencyBins
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121 "150,200,250,300,350" --IgnoreGaps Yes Sample1.aln
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122
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123 AUTHOR
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124 Manish Sud <msud@san.rr.com>
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125
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126 SEE ALSO
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127 AnalyzeSequenceFilesData.pl, ExtractFromSequenceFiles.pl,
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128 InfoAminoAcids.pl, InfoNucleicAcids.pl
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129
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130 COPYRIGHT
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131 Copyright (C) 2015 Manish Sud. All rights reserved.
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132
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133 This file is part of MayaChemTools.
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134
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135 MayaChemTools is free software; you can redistribute it and/or modify it
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136 under the terms of the GNU Lesser General Public License as published by
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137 the Free Software Foundation; either version 3 of the License, or (at
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138 your option) any later version.
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139
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