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1 #!/usr/bin/perl -w
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2 #
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3 # This script extracts sequences from a multi-sequence FASTA file
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4 # based on a list of accession numbers / IDs
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5 #
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6 # =====================================================
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7 # $Id: ExtractSeqsFromFasta.pl 15 2010-07-08 18:07:59Z pieter $
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8 # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ExtractSeqsFromFasta.pl $
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9 # $LastChangedDate: 2010-07-08 13:07:59 -0500 (Thu, 08 Jul 2010) $
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10 # $LastChangedRevision: 15 $
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11 # $LastChangedBy: pieter $
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12 # =====================================================
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13
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14 #
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15 # initialise environment
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16 #
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17 use strict;
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18 use Getopt::Std;
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19 use Log::Log4perl qw(:easy);
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20
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21 my %log_levels = (
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22 'ALL' => $ALL,
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23 'TRACE' => $TRACE,
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24 'DEBUG' => $DEBUG,
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25 'INFO' => $INFO,
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26 'WARN' => $WARN,
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27 'ERROR' => $ERROR,
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28 'FATAL' => $FATAL,
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29 'OFF' => $OFF,
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30 );
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31 my %match_logic_types = (
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32 'literal' => 1,
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33 'regex' => 1,
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34 );
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35
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36 #
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37 # Get options.
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38 #
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39 my %opts;
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40 Getopt::Std::getopts('ul:i:o:f:m:', \%opts);
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41
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42 my $input = $opts{'i'};
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43 my $output = $opts{'o'};
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44 my $filter = $opts{'f'};
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45 my $log_level = $opts{'l'};
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46 my $match_logic = $opts{'m'};
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47 my $ignore_accession_version = $opts{'u'};
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48
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49 #
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50 # Configure logging.
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51 #
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52 # Provides default if user did not specify log level:
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53 $log_level = (defined($log_level) ? $log_level : 'INFO');
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54
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55 # Reset log level to default if user specified illegal log level.
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56 $log_level = (
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57 defined($log_levels{$log_level})
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58 ? $log_levels{$log_level}
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59 : $log_levels{'INFO'});
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60
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61 #Log::Log4perl->init('log4perl.properties');
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62 Log::Log4perl->easy_init(
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63
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64 #{ level => $log_level,
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65 # file => ">>ExtractSeqsFromFasta.log",
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66 # layout => '%F{1}-%L-%M: %m%n' },
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67 {
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68 level => $log_level,
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69 file => "STDOUT",
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70 layout => '%d L:%L %p> %m%n'
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71 },
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72 );
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73 my $logger = Log::Log4perl::get_logger();
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74
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75 #
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76 # Check user input.
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77 #
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78 unless (defined($input) && defined($output) && defined($filter)) {
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79 _Usage();
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80 exit;
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81 }
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82 if ($input =~ /^$/ || $output =~ /^$/ || $filter =~ /^$/) {
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83 _Usage();
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84 exit;
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85 }
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86 if ($input eq $output) {
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87 $logger->fatal('Output file is the same as the input file. Select a different file for the output.');
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88 exit;
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89 }
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90
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91 #
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92 # Check input and filter file.
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93 #
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94 unless (-e $input && -f $input && -r $input) {
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95 $logger->fatal('Cannot read from input file ' . $input . ': ' . $!);
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96 exit;
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97 }
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98 unless (-e $filter && -f $filter && -r $filter) {
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99 $logger->fatal('Cannot read from filter file ' . $filter . ': ' . $!);
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100 exit;
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101 }
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102 #
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103 # Check match logic.
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104 #
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105 $match_logic = (defined($match_logic) ? $match_logic : 'literal');
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106 unless (defined($match_logic_types{$match_logic})) {
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107 $logger->fatal('Unkown logic ' . $match_logic . ' specified for filtering of the input sequences.');
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108 exit;
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109 }
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110
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111 #
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112 # Read accession numbers to search the FASTA file(s) for
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113 #
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114 my $wanted = _CreateLookupHash($filter, $match_logic);
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115 my $seqs_to_extract = scalar(keys(%{$wanted}));
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116 $logger->info('Number of sequences to search for: ' . $seqs_to_extract);
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117
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118 #
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119 # Extract seqs
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120 #
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121 my ($counter) = _ExtractSeqs($input, $output, $wanted, $match_logic);
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122
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123 $logger->info('Extracted ' . $counter . ' sequences.');
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124 $logger->info('Finished!');
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125
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126 #
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127 ##
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128 ### Internal subs.
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129 ##
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130 #
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131
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132 sub _CreateLookupHash {
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133
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134 my ($file_path, $match_logic) = @_;
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135
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136 $logger->info('Parsing ' . $file_path . '...');
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137
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138 my %wanted;
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139 my $file_path_fh;
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140
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141 eval {
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142 open($file_path_fh, "<$file_path");
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143 };
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144 if ($@) {
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145 $logger->fatal('Cannot read ID file: ' . $@);
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146 exit;
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147 }
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148
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149 LINE: while (my $line = <$file_path_fh>) {
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150
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151 $line =~ s/[\r\n]+//g;
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152
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153 if ($match_logic eq 'literal') {
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154
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155 if ($line =~ m/([a-z0-9_\-\.]+)/i) {
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156
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157 my $id = $1;
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158
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159 if ($ignore_accession_version) {
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160
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161 #
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162 # Remove version from accession number if it was versioned.
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163 #
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164 if ($id =~ m/([^\.]+)\.(\d+)/) {
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165
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166 $id = $1;
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167
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168 }
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169 }
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170
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171 $logger->debug('Found accession/ID ' . $id);
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172 $wanted{$id} = 1;
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173
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174 } else {
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175 $logger->warn('Accession/ID in unsupported format: ' . $line);
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176 next;
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177 }
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178
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179 } elsif ($match_logic eq 'regex') {
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180
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181 if ($line =~ m/([a-z0-9_\-\.\[\]:?^\$]+)/i) {
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182 my $regex = $1;
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183 $logger->debug('Found regex ' . $regex);
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184 $wanted{$regex} = 1;
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185 } else {
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186 $logger->warn('Regex in unsupported format: ' . $line);
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187 next;
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188 }
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189
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190 }
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191 }
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192
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193 close($file_path_fh);
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194 $logger->info('Created ID lookup list.');
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195
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196 return (\%wanted);
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197
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198 }
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199
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200 sub _ExtractSeqs {
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201
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202 my ($path_from, $path_to, $wanted, $match_logic) = @_;
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203
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204 $logger->info('Parsing ' . $path_from . '...');
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205
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206 my $extracted_seqs = 0;
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207 my $found = 0;
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208 my $path_from_fh;
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209 my $path_to_fh;
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210
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211 eval {
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212 open($path_from_fh, "<$path_from");
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213 };
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214 if ($@) {
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215 $logger->fatal('Cannot read FASTA file: ' . $@);
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216 exit;
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217 }
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218 eval {
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219 open($path_to_fh, ">$path_to");
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220 };
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221 if ($@) {
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222 $logger->fatal('Cannot write FASTA file: ' . $@);
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223 exit;
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224 }
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225
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226 LINE: while (my $line = <$path_from_fh>) {
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227
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228 if ($line =~ m/^>/) {
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229 $logger->debug('Found header line: ' . $line);
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230 $found = 0;
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231 my @header_ids;
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232
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233 #
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234 # Check for the presence of some frequently occurring naming schemes:
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235 #
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236 # >IPI:CON_Trypsin|SWISS-PROT:P00761|TRYP_PIG Trypsin - Sus scrofa (Pig).
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237 # >IPI:CON_IPI00174775.2|TREMBL:Q32MB2;Q86Y46 Tax_Id=9606 Gene_Symbol=KRT73 Keratin-73
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238 # >sp|Q42592|APXS_ARATH L-ascorbate peroxidase S, chloroplastic/mitochondrial;
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239 # >jgi|Triad1|1|gw1.3.1.1
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240 #
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241 if ($line =~ m/^>((([^\s\n\r:;|]+)[:]([^\s\n\r:|]+)[|;])*([^\s\n\r:;|]+)[:]([^\s\n\r:|]+))[|;]?(\s+(.+))?/i) {
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242
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243 #
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244 # One or more namespace prefixed IDs.
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245 #
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246 my $concatenated_namespace_prefixed_ids = $1;
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247 $logger->debug('Found prefixed IDs in header: ' . $concatenated_namespace_prefixed_ids);
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248
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249 # database_namespace = $3 && $5;
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250 # id = $4 && $6;
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251 # description = $8;
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252 my @namespace_prefixed_ids = split(/[|;]/, $concatenated_namespace_prefixed_ids);
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253
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254 foreach my $prefixed_id (@namespace_prefixed_ids) {
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255
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256 if ($prefixed_id =~ m/([^\s\n\r:;|]+:)?([^\s\n\r:|]+)/i) {
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257
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258 my $this_id = $2;
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259
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260 $logger->debug('Found ID: ' . $this_id);
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261 push(@header_ids, $this_id);
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262
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263 } else {
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264
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265 $logger->warn(
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266 'This should have been an optionally prefixed ID, '
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267 . 'but failed to match the corresponding regex: '
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268 . $prefixed_id);
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269
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270 }
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271 }
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272
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273 } elsif ($line =~ m/^>((([^\s\n\r:;|]+)[|;])*([^\s\n\r:;|]+))[|;]?(\s+(.+))?/i) {
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274
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275 #
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276 # One or more unprefixed IDs.
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277 #
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278 my $concatenated_ids = $1;
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279 $logger->debug('Found unprefixed IDs in header: ' . $concatenated_ids);
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280
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281 # id = $3 && $4;
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282 # description = $7;
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283 my @unprefixed_ids = split(/[|;]/, $concatenated_ids);
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284
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285 foreach my $unprefixed_id (@unprefixed_ids) {
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286
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287 $logger->debug('Found ID: ' . $unprefixed_id);
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288 push(@header_ids, $unprefixed_id);
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289
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290 }
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291
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292 } else {
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293
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294 #
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295 # Something else.
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296 #
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297 # The FASTA header line can basically have any format,
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298 # so this is probably one of the less frequent occurring annotation schemes.
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299 # Therefore we try to see if the IDs we are looking for are present anywhere
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300 # in the header line up until the first white space or new line.
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301 # This may be tricky as we might match other annotation from other proteins
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302 # like a description from a 'best' BLAST hit that contains one of the IDs we
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303 # are looking for. Hence, in such a case this sequence is *not* the one of
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304 # the IDs we looking for, but similar to that one at best.
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305 #
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306 if ($line =~ m/>([^\n\r\s]+)/) {
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307
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308 my $putative_id = $1;
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309 $logger->debug('Found putative ID in header: ' . $putative_id);
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310 push(@header_ids, $putative_id);
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311
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312 } else {
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313 $logger->warn('Cannot identify IDs in this header: ' . $line);
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314 }
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315 }
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316
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317
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318 if ($ignore_accession_version) {
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319
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320 for my $inx (0 .. $#header_ids) {
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321
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322 if ($header_ids[$inx] =~ m/([^\.]+)\.(\d+)/) {
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323
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324 my $this_unversioned_id = $1;
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325 my $version_number = $2;
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326 $logger->debug('Dropping version number (' . $version_number . ') for versioned ID: ' . $this_unversioned_id . '.');
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327 $header_ids[$inx] = $this_unversioned_id;
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328
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329 }
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330 }
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331 }
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332
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333 foreach my $id (@header_ids) {
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334 $logger->debug('Checking if ID ' . $id . ' is in the list of sequences to extract.');
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335
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336 if ($match_logic eq 'literal') {
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337
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338 if (${$wanted}{$id}) {
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339 $logger->info('Literal bingo, preserving sequence with ID ' . $id);
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340 $found = 1;
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341 $extracted_seqs++;
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342 last;
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343 }
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344
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345 } elsif ($match_logic eq 'regex') {
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346
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347 foreach my $regex (keys(%{$wanted})) {
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348
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349 if ($id =~ m/$regex/) {
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350 $logger->info('Regex bingo, preserving sequence with ID ' . $id);
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351 $found = 1;
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352 $extracted_seqs++;
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353 last;
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354 }
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355 }
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356 }
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357 }
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358 }
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359 if ($found) {
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360 print($path_to_fh $line);
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361 }
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362
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363 }
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364
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365 close($path_from_fh);
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366 close($path_to_fh);
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367
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368 return ($extracted_seqs);
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369
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370 }
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371
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372 sub _Usage {
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373
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374 print STDERR "\n"
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375 . "extractSeqsFromFasta.pl:\n"
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376 . " Extracts sequences from a multi-sequence FASTA file.\n" . "\n"
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377 . "Usage:\n" . "\n"
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378 . " extractSeqsFromFasta.pl options\n" . "\n"
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379 . "Available options are:\n" . "\n"
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380 . " -i [file] Input file in FASTA format.\n"
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381 . " -o [file] Output file in FASTA format where the extracted files will be saved.\n"
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382 . " -f [file] Filter file containing accession numbers or IDs that shoud be extracted from the input.\n"
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383 . " (One accession/ID per line)\n"
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384 . " -m [string] Match logic that defines how the accession numbers or IDs from the filter file will be.\n"
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385 . " matched to those in the FASTA file. Supported logic types:\n"
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386 . " literal for exact matching.\n"
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387 . " regex for fuzzy matching using simple regular expressions (in Perl regex syntax).\n"
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388 . " -u Use unversioned accession numbers for matching (only with -m literal).\n"
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389 . " If the FASTA input file contains a versioned accession number like this IPI00189968.5,\n"
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390 . " running this tool without -u (default) IPI00189968 or IPI00189968.2 will not match IPI00189968.5, \n"
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391 . " but with -u IPI00189968 or IPI00189968.2 will match IPI00189968.5 and the sequence will be extracted.\n"
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392 . " Hence this allows for less strict matching, but is less fuzzy than matching with regexes.\n"
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393 . " -l [LEVEL] Log4perl log level. One of: ALL, TRACE, DEBUG, INFO (default), WARN, ERROR, FATAL or OFF.\n"
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394 . "\n";
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395 exit;
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396
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397 }
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