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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: InfoSequenceFiles.pl,v $
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4 # $Date: 2015/02/28 20:46:20 $
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5 # $Revision: 1.29 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use FindBin; use lib "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SequenceFileUtil;
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38 use StatisticsUtil;
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39
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40 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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41
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42 # Autoflush STDOUT
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43 $| = 1;
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44
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45 # Starting message...
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46 $ScriptName = basename($0);
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47 print "\n$ScriptName: Starting...\n\n";
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48 $StartTime = new Benchmark;
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49
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50 # Get the options and setup script...
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51 SetupScriptUsage();
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52 if ($Options{help} || @ARGV < 1) {
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53 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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54 }
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55
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56 my(@SequenceFilesList);
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57 @SequenceFilesList = ExpandFileNames(\@ARGV, "aln msf fasta fta pir");
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58
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59 print "Processing options...\n";
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60 my(%OptionsInfo);
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61 ProcessOptions();
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62
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63 print "Checking input sequence file(s)...\n";
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64 my(%SequenceFilesInfo);
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65 RetrieveSequenceFilesInfo();
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66
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67 my($FileIndex);
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68 if (@SequenceFilesList > 1) {
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69 print "\nProcessing sequence files...\n";
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70 }
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71 for $FileIndex (0 .. $#SequenceFilesList) {
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72 if ($SequenceFilesInfo{FileOkay}[$FileIndex]) {
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73 print "\nProcessing file $SequenceFilesList[$FileIndex]...\n";
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74 ListSequenceFileInfo($FileIndex);
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75 }
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76 }
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77 ListTotalSizeOfFiles();
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78
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79 print "\n$ScriptName:Done...\n\n";
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80
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81 $EndTime = new Benchmark;
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82 $TotalTime = timediff ($EndTime, $StartTime);
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83 print "Total time: ", timestr($TotalTime), "\n";
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84
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85 ###############################################################################
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86
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87 # List appropriate information...
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88 sub ListSequenceFileInfo {
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89 my($Index) = @_;
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90 my($SequenceFile, $SequenceDataRef);
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91
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92 $SequenceFile = $SequenceFilesList[$Index];
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93
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94 $SequenceDataRef = ReadSequenceFile($SequenceFile);
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95
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96 my($SequencesCount) = $SequenceDataRef->{Count};
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97 print "\nNumber of sequences: $SequencesCount\n";
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98
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99 if ($OptionsInfo{ListShortestSequence} && ($SequencesCount > 1)) {
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100 my($ShortestSeqID, $ShortestSeq, $ShortestSeqLen, $Description) = GetShortestSequence($SequenceDataRef, $OptionsInfo{IgnoreGaps});
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101 print "\nShortest sequence information:\nID: $ShortestSeqID; Length:$ShortestSeqLen\n";
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102 if ($OptionsInfo{DetailLevel} >= 2) {
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103 print "Description: $Description\n";
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104 }
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105 if ($OptionsInfo{DetailLevel} >= 3) {
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106 print "Sequence: $ShortestSeq\n";
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107 }
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108 }
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109 if ($OptionsInfo{ListLongestSequence} && ($SequencesCount > 1)) {
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110 my($LongestSeqID, $LongestSeq, $LongestSeqLen, $Description) = GetLongestSequence($SequenceDataRef, $OptionsInfo{IgnoreGaps});
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111 print "\nLongest sequence information:\nID: $LongestSeqID; Length: $LongestSeqLen\n";
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112 if ($OptionsInfo{DetailLevel} >= 2) {
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113 print "Description: $Description\n";
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114 }
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115 if ($OptionsInfo{DetailLevel} >= 3) {
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116 print "Sequence: $LongestSeq\n";
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117 }
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118 }
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119 if ($OptionsInfo{FrequencyAnalysis} && ($SequencesCount > 1)) {
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120 PerformLengthFrequencyAnalysis($SequenceDataRef);
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121 }
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122 if ($OptionsInfo{ListSequenceLengths}) {
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123 ListSequenceLengths($SequenceDataRef);
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124 }
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125
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126 # File size and modification information...
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127 print "\nFile size: ", FormatFileSize($SequenceFilesInfo{FileSize}[$Index]), " \n";
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128 print "Last modified: ", $SequenceFilesInfo{FileLastModified}[$Index], " \n";
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129 }
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130
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131 # List information about sequence lengths...
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132 sub ListSequenceLengths {
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133 my($SequenceDataRef) = @_;
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134 my($ID, $SeqLen, $Sequence, $Description);
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135
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136 print "\nSequence lengths information:\n";
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137 for $ID (@{$SequenceDataRef->{IDs}}) {
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138 $Sequence = $SequenceDataRef->{Sequence}{$ID};
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139 $Description = $SequenceDataRef->{Description}{$ID};
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140 $SeqLen = GetSequenceLength($Sequence, $OptionsInfo{IgnoreGaps});
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141 if ($OptionsInfo{IgnoreGaps}) {
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142 $Sequence = RemoveSequenceGaps($Sequence);
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143 }
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144 print "ID: $ID; Length:$SeqLen\n";
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145 if ($OptionsInfo{DetailLevel} >= 2) {
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146 print "Description: $Description\n";
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147 }
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148 if ($OptionsInfo{DetailLevel} >= 3) {
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149 print "Sequence: $Sequence\n";
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150 }
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151 if ($OptionsInfo{DetailLevel} >= 2) {
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152 print "\n";
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153 }
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154 }
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155 }
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156
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157 # Total size of all the fiels...
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158 sub ListTotalSizeOfFiles {
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159 my($FileOkayCount, $TotalSize, $Index);
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160
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161 $FileOkayCount = 0;
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162 $TotalSize = 0;
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163
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164 for $Index (0 .. $#SequenceFilesList) {
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165 if ($SequenceFilesInfo{FileOkay}[$Index]) {
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166 $FileOkayCount++;
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167 $TotalSize += $SequenceFilesInfo{FileSize}[$Index];
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168 }
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169 }
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170 if ($FileOkayCount > 1) {
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171 print "\nTotal size of $FileOkayCount files: ", FormatFileSize($TotalSize), "\n";
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172 }
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173 }
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174
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175
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176 # Perform frequency analysis of sequence lengths
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177 sub PerformLengthFrequencyAnalysis {
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178 my($SequenceDataRef, $SequenceLengthsRef) = @_;
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179 my ($ID, $SeqLen, $Sequence, $SequenceLenBin, $LenBin, $SequenceLenCount, @SequenceLengths, %SequenceLenFrequency);
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180
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181 @SequenceLengths = ();
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182 %SequenceLenFrequency = ();
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183 for $ID (@{$SequenceDataRef->{IDs}}) {
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184 $Sequence = $SequenceDataRef->{Sequence}{$ID};
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185 $SeqLen = GetSequenceLength($Sequence, $OptionsInfo{IgnoreGaps});
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186 push @SequenceLengths, $SeqLen;
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187 }
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188 if (@{$OptionsInfo{BinRange}}) {
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189 %SequenceLenFrequency = Frequency(\@SequenceLengths, \@{$OptionsInfo{BinRange}});
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190 }
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191 else {
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192 %SequenceLenFrequency = Frequency(\@SequenceLengths, $OptionsInfo{NumOfBins});
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193 }
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194 print "\nDistribution of sequence lengths (LengthBin => Count):\n";
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195 for $SequenceLenBin (sort { $a <=> $b} keys %SequenceLenFrequency) {
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196 $SequenceLenCount = $SequenceLenFrequency{$SequenceLenBin};
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197 $LenBin = sprintf("%.1f", $SequenceLenBin) + 0;
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198 print "$LenBin => $SequenceLenCount; ";
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199 }
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200 print "\n";
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201 }
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202
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203 # Retrieve information about sequence files...
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204 sub RetrieveSequenceFilesInfo {
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205 my($Index, $SequenceFile, $FileSupported, $FileFormat, $ModifiedTimeString, $ModifiedDateString);
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206
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207 %SequenceFilesInfo = ();
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208 @{$SequenceFilesInfo{FileOkay}} = ();
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209 @{$SequenceFilesInfo{FileFormat}} = ();
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210 @{$SequenceFilesInfo{FileSize}} = ();
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211 @{$SequenceFilesInfo{FileLastModified}} = ();
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212
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213 FILELIST: for $Index (0 .. $#SequenceFilesList) {
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214 $SequenceFile = $SequenceFilesList[$Index];
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215
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216 if (! open SEQUENCEFILE, "$SequenceFile") {
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217 warn "Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n";
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218 next FILELIST;
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219 }
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220 close SEQUENCEFILE;
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221
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222 $SequenceFilesInfo{FileOkay}[$Index] = 0;
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223 $SequenceFilesInfo{FileFormat}[$Index] = 'NotSupported';
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224 $SequenceFilesInfo{FileSize}[$Index] = 0;
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225 $SequenceFilesInfo{FileLastModified}[$Index] = '';
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226
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227 ($FileSupported, $FileFormat) = IsSupportedSequenceFile($SequenceFile);
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228 if (!$FileSupported) {
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229 warn "Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n";
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230 next FILELIST;
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231 }
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232
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233 $SequenceFilesInfo{FileOkay}[$Index] = 1;
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234 $SequenceFilesInfo{FileFormat}[$Index] = $FileFormat;
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235 $SequenceFilesInfo{FileSize}[$Index] = FileSize($SequenceFile);
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236
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237 ($ModifiedTimeString, $ModifiedDateString) = FormattedFileModificationTimeAndDate($SequenceFile);
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238 $SequenceFilesInfo{FileLastModified}[$Index] = "$ModifiedTimeString; $ModifiedDateString";
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239 }
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240 }
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241
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242 # Process option values...
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243 sub ProcessOptions {
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244
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245 $OptionsInfo{All} = defined $Options{all} ? $Options{all} : undef;
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246
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247 $OptionsInfo{Count} = defined $Options{count} ? $Options{count} : undef;
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248 $OptionsInfo{DetailLevel} = $Options{detail};
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249 $OptionsInfo{Frequency} = defined $Options{frequency} ? $Options{frequency} : undef;
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250 $OptionsInfo{FrequencyBins} = defined $Options{frequencybins} ? $Options{frequencybins} : undef;
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251 $OptionsInfo{IgnoreGaps} = defined $Options{ignoregaps} ? $Options{ignoregaps} : undef;
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252 $OptionsInfo{Longest} = defined $Options{longest} ? $Options{longest} : undef;
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253 $OptionsInfo{Shortest} = defined $Options{shortest} ? $Options{shortest} : undef;
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254 $OptionsInfo{SequenceLengths} = defined $Options{sequencelengths} ? $Options{sequencelengths} : undef;
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255
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256 $OptionsInfo{FrequencyAnalysis} = ($Options{all} || $Options{frequency}) ? 1 : 0;
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257 $OptionsInfo{ListLongestSequence} = ($Options{all} || $Options{longest}) ? 1 : 0;
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258 $OptionsInfo{ListShortestSequence} = ($Options{all} || $Options{shortest}) ? 1 : 0;
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259 $OptionsInfo{ListSequenceLengths} = ($Options{all} || $Options{sequencelengths}) ? 1 : 0;
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260 $OptionsInfo{IgnoreGaps} = ($Options{ignoregaps} =~ /Yes/i) ? 1 : 0;
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261
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262 # Setup frequency bin values...
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263 $OptionsInfo{NumOfBins} = 4;
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264 @{$OptionsInfo{BinRange}} = ();
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265
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266 if ($Options{frequencybins} =~ /\,/) {
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267 my($BinValue, @SpecifiedBinRange);
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268 @SpecifiedBinRange = split /\,/, $Options{frequencybins};
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269 if (@SpecifiedBinRange < 2) {
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270 die "Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Must contain at least two values. \n";
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271 }
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272 for $BinValue (@SpecifiedBinRange) {
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273 if (!IsNumerical($BinValue)) {
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274 die "Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Contains non numeric values. \n";
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275 }
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276 }
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277 my($Index1, $Index2);
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278 for $Index1 (0 .. $#SpecifiedBinRange) {
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279 for $Index2 (($Index1 + 1) .. $#SpecifiedBinRange) {
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280 if ($SpecifiedBinRange[$Index1] >= $SpecifiedBinRange[$Index2]) {
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281 die "Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Must contain values in ascending order. \n";
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282 }
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283 }
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284 }
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285 push @{$OptionsInfo{BinRange}}, @SpecifiedBinRange;
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286 }
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287 else {
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288 $OptionsInfo{NumOfBins} = $Options{frequencybins};
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289 if (!IsPositiveInteger($OptionsInfo{NumOfBins})) {
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290 die "Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid. Allowed values: positive integer or \"number,number,[number]...\". \n";
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291 }
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292 }
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293 }
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294
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295 # Setup script usage and retrieve command line arguments specified using various options...
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296 sub SetupScriptUsage {
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297
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298 # Retrieve all the options...
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299 %Options = ();
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300 $Options{detail} = 1;
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301 $Options{ignoregaps} = 'no';
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302 $Options{frequencybins} = 10;
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303
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304 if (!GetOptions(\%Options, "all|a", "count|c", "detail|d=i", "frequency|f", "frequencybins=s", "help|h", "ignoregaps|i=s", "longest|l", "shortest|s", "sequencelengths", "workingdir|w=s")) {
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305 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
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306 }
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307 if ($Options{workingdir}) {
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308 if (! -d $Options{workingdir}) {
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309 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
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310 }
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311 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
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312 }
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313 if (!IsPositiveInteger($Options{detail})) {
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314 die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
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315 }
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316 if ($Options{ignoregaps} !~ /^(yes|no)$/i) {
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317 die "Error: The value specified, $Options{ignoregaps}, for option \"-i --IgnoreGaps\" is not valid. Allowed values: yes or no\n";
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318 }
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319 }
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320
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321 __END__
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322
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323 =head1 NAME
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324
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325 InfoSequenceFiles.pl - List information about sequence and alignment files
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326
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327 =head1 SYNOPSIS
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328
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329 InfoSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...
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330
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331 InfoSequenceFiles.pl [B<-a, --all>] [B<-c, --count>] [B<-d, --detail> infolevel]
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332 [B<-f, --frequency>] [B<--FrequencyBins> number | "number, number, [number,...]"]
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333 [B<-h, --help>] [B<-i, --IgnoreGaps> yes | no] [B<-l, --longest>] [B<-s, --shortest>]
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334 [B<--SequenceLengths>] [B<-w, --workingdir> dirname] SequenceFile(s)...
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335
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336 =head1 DESCRIPTION
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337
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338 List information about contents of I<SequenceFile(s) and AlignmentFile(s)>: number of sequences,
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339 shortest and longest sequences, distribution of sequence lengths and so on. The file names are
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340 separated by spaces. All the sequence files in a current directory can be specified by I<*.aln>,
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341 I<*.msf>, I<*.fasta>, I<*.fta>, I<*.pir> or any other supported formats; additionally, I<DirName>
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342 corresponds to all the sequence files in the current directory with any of the supported file
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343 extension: I<.aln, .msf, .fasta, .fta, and .pir>.
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344
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345 Supported sequence formats are: I<ALN/CLustalW>, I<GCG/MSF>, I<PILEUP/MSF>, I<Pearson/FASTA>,
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346 and I<NBRF/PIR>. Instead of using file extensions, file formats are detected by parsing the contents
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347 of I<SequenceFile(s) and AlignmentFile(s)>.
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348
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349 =head1 OPTIONS
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350
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351 =over 4
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352
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353 =item B<-a, --all>
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354
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355 List all the available information.
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356
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357 =item B<-c, --count>
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358
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359 List number of of sequences. This is B<default behavior>.
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360
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361 =item B<-d, --detail> I<InfoLevel>
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362
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363 Level of information to print about sequences during various options. Default: I<1>.
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364 Possible values: I<1, 2 or 3>.
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365
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366 =item B<-f, --frequency>
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367
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368 List distribution of sequence lengths using the specified number of bins or bin range specified
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369 using B<FrequencyBins> option.
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370
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371 This option is ignored for input files containing only single sequence.
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372
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373 =item B<--FrequencyBins> I<number | "number,number,[number,...]">
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374
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375 This value is used with B<-f, --frequency> option to list distribution of sequence lengths using
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376 the specified number of bins or bin range. Default value: I<10>.
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377
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378 The bin range list is used to group sequence lengths into different groups; It must contain
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379 values in ascending order. Examples:
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380
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381 100,200,300,400,500,600
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382 200,400,600,800,1000
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383
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384 The frequency value calculated for a specific bin corresponds to all the sequence lengths
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385 which are greater than the previous bin value and less than or equal to the current bin value.
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386
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387 =item B<-h, --help>
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388
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389 Print this help message.
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390
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391 =item B<-i, --IgnoreGaps> I<yes | no>
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392
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393 Ignore gaps during calculation of sequence lengths. Possible values: I<yes or
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394 no>. Default value: I<no>.
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395
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396 =item B<-l, --longest>
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397
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398 List information about longest sequence: ID, sequence and sequence length. This option
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399 is ignored for input files containing only single sequence.
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400
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401 =item B<-s, --shortest>
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402
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403 List information about shortest sequence: ID, sequence and sequence length. This option
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404 is ignored for input files containing only single sequence.
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405
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406 =item B<--SequenceLengths>
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407
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408 List information about sequence lengths.
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409
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410 =item B<-w, --WorkingDir> I<dirname>
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411
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412 Location of working directory. Default: current directory.
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413
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414 =back
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415
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416 =head1 EXAMPLES
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417
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418 To count number of sequences in sequence files, type:
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419
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420 % InfoSequenceFiles.pl Sample1.fasta
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421 % InfoSequenceFiles.pl Sample1.msf Sample1.aln Sample1.pir
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422 % InfoSequenceFiles.pl *.fasta *.fta *.msf *.pir *.aln
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423
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424 To list all available information with maximum level of available detail for a sequence
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425 alignment file Sample1.msf, type:
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426
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427 % InfoSequenceFiles.pl -a -d 3 Sample1.msf
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428
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429 To list sequence length information after ignoring sequence gaps in Sample1.aln file, type:
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430
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431 % InfoSequenceFiles.pl --SequenceLengths --IgnoreGaps Yes
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432 Sample1.aln
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433
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434 To list shortest and longest sequence length information after ignoring sequence
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435 gaps in Sample1.aln file, type:
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436
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437 % InfoSequenceFiles.pl --longest --shortest --IgnoreGaps Yes
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438 Sample1.aln
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439
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440 To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and
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441 report the frequency distribution into 10 bins, type:
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442
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443 % InfoSequenceFiles.pl --frequency --FrequencyBins 10
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444 --IgnoreGaps Yes Sample1.aln
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445
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446 To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and
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447 report the frequency distribution into specified bin range, type:
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448
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449 % InfoSequenceFiles.pl --frequency --FrequencyBins
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450 "150,200,250,300,350" --IgnoreGaps Yes Sample1.aln
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451
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452 =head1 AUTHOR
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453
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454 Manish Sud <msud@san.rr.com>
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455
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456 =head1 SEE ALSO
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457
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458 AnalyzeSequenceFilesData.pl, ExtractFromSequenceFiles.pl, InfoAminoAcids.pl, InfoNucleicAcids.pl
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459
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460 =head1 COPYRIGHT
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461
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462 Copyright (C) 2015 Manish Sud. All rights reserved.
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463
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464 This file is part of MayaChemTools.
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465
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466 MayaChemTools is free software; you can redistribute it and/or modify it under
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467 the terms of the GNU Lesser General Public License as published by the Free
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468 Software Foundation; either version 3 of the License, or (at your option)
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469 any later version.
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470
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471 =cut
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