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author galaxyp
date Fri, 10 May 2013 17:15:08 -0400
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1 #!/usr/bin/perl -w
2 #
3 # This script extracts sequences from a multi-sequence FASTA file
4 # based on a list of accession numbers / IDs
5 #
6 # =====================================================
7 # $Id: ExtractSeqsFromFasta.pl 15 2010-07-08 18:07:59Z pieter $
8 # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ExtractSeqsFromFasta.pl $
9 # $LastChangedDate: 2010-07-08 13:07:59 -0500 (Thu, 08 Jul 2010) $
10 # $LastChangedRevision: 15 $
11 # $LastChangedBy: pieter $
12 # =====================================================
13
14 #
15 # initialise environment
16 #
17 use strict;
18 use Getopt::Std;
19 use Log::Log4perl qw(:easy);
20
21 my %log_levels = (
22 'ALL' => $ALL,
23 'TRACE' => $TRACE,
24 'DEBUG' => $DEBUG,
25 'INFO' => $INFO,
26 'WARN' => $WARN,
27 'ERROR' => $ERROR,
28 'FATAL' => $FATAL,
29 'OFF' => $OFF,
30 );
31 my %match_logic_types = (
32 'literal' => 1,
33 'regex' => 1,
34 );
35
36 #
37 # Get options.
38 #
39 my %opts;
40 Getopt::Std::getopts('ul:i:o:f:m:', \%opts);
41
42 my $input = $opts{'i'};
43 my $output = $opts{'o'};
44 my $filter = $opts{'f'};
45 my $log_level = $opts{'l'};
46 my $match_logic = $opts{'m'};
47 my $ignore_accession_version = $opts{'u'};
48
49 #
50 # Configure logging.
51 #
52 # Provides default if user did not specify log level:
53 $log_level = (defined($log_level) ? $log_level : 'INFO');
54
55 # Reset log level to default if user specified illegal log level.
56 $log_level = (
57 defined($log_levels{$log_level})
58 ? $log_levels{$log_level}
59 : $log_levels{'INFO'});
60
61 #Log::Log4perl->init('log4perl.properties');
62 Log::Log4perl->easy_init(
63
64 #{ level => $log_level,
65 # file => ">>ExtractSeqsFromFasta.log",
66 # layout => '%F{1}-%L-%M: %m%n' },
67 {
68 level => $log_level,
69 file => "STDOUT",
70 layout => '%d L:%L %p> %m%n'
71 },
72 );
73 my $logger = Log::Log4perl::get_logger();
74
75 #
76 # Check user input.
77 #
78 unless (defined($input) && defined($output) && defined($filter)) {
79 _Usage();
80 exit;
81 }
82 if ($input =~ /^$/ || $output =~ /^$/ || $filter =~ /^$/) {
83 _Usage();
84 exit;
85 }
86 if ($input eq $output) {
87 $logger->fatal('Output file is the same as the input file. Select a different file for the output.');
88 exit;
89 }
90
91 #
92 # Check input and filter file.
93 #
94 unless (-e $input && -f $input && -r $input) {
95 $logger->fatal('Cannot read from input file ' . $input . ': ' . $!);
96 exit;
97 }
98 unless (-e $filter && -f $filter && -r $filter) {
99 $logger->fatal('Cannot read from filter file ' . $filter . ': ' . $!);
100 exit;
101 }
102 #
103 # Check match logic.
104 #
105 $match_logic = (defined($match_logic) ? $match_logic : 'literal');
106 unless (defined($match_logic_types{$match_logic})) {
107 $logger->fatal('Unkown logic ' . $match_logic . ' specified for filtering of the input sequences.');
108 exit;
109 }
110
111 #
112 # Read accession numbers to search the FASTA file(s) for
113 #
114 my $wanted = _CreateLookupHash($filter, $match_logic);
115 my $seqs_to_extract = scalar(keys(%{$wanted}));
116 $logger->info('Number of sequences to search for: ' . $seqs_to_extract);
117
118 #
119 # Extract seqs
120 #
121 my ($counter) = _ExtractSeqs($input, $output, $wanted, $match_logic);
122
123 $logger->info('Extracted ' . $counter . ' sequences.');
124 $logger->info('Finished!');
125
126 #
127 ##
128 ### Internal subs.
129 ##
130 #
131
132 sub _CreateLookupHash {
133
134 my ($file_path, $match_logic) = @_;
135
136 $logger->info('Parsing ' . $file_path . '...');
137
138 my %wanted;
139 my $file_path_fh;
140
141 eval {
142 open($file_path_fh, "<$file_path");
143 };
144 if ($@) {
145 $logger->fatal('Cannot read ID file: ' . $@);
146 exit;
147 }
148
149 LINE: while (my $line = <$file_path_fh>) {
150
151 $line =~ s/[\r\n]+//g;
152
153 if ($match_logic eq 'literal') {
154
155 if ($line =~ m/([a-z0-9_\-\.]+)/i) {
156
157 my $id = $1;
158
159 if ($ignore_accession_version) {
160
161 #
162 # Remove version from accession number if it was versioned.
163 #
164 if ($id =~ m/([^\.]+)\.(\d+)/) {
165
166 $id = $1;
167
168 }
169 }
170
171 $logger->debug('Found accession/ID ' . $id);
172 $wanted{$id} = 1;
173
174 } else {
175 $logger->warn('Accession/ID in unsupported format: ' . $line);
176 next;
177 }
178
179 } elsif ($match_logic eq 'regex') {
180
181 if ($line =~ m/([a-z0-9_\-\.\[\]:?^\$]+)/i) {
182 my $regex = $1;
183 $logger->debug('Found regex ' . $regex);
184 $wanted{$regex} = 1;
185 } else {
186 $logger->warn('Regex in unsupported format: ' . $line);
187 next;
188 }
189
190 }
191 }
192
193 close($file_path_fh);
194 $logger->info('Created ID lookup list.');
195
196 return (\%wanted);
197
198 }
199
200 sub _ExtractSeqs {
201
202 my ($path_from, $path_to, $wanted, $match_logic) = @_;
203
204 $logger->info('Parsing ' . $path_from . '...');
205
206 my $extracted_seqs = 0;
207 my $found = 0;
208 my $path_from_fh;
209 my $path_to_fh;
210
211 eval {
212 open($path_from_fh, "<$path_from");
213 };
214 if ($@) {
215 $logger->fatal('Cannot read FASTA file: ' . $@);
216 exit;
217 }
218 eval {
219 open($path_to_fh, ">$path_to");
220 };
221 if ($@) {
222 $logger->fatal('Cannot write FASTA file: ' . $@);
223 exit;
224 }
225
226 LINE: while (my $line = <$path_from_fh>) {
227
228 if ($line =~ m/^>/) {
229 $logger->debug('Found header line: ' . $line);
230 $found = 0;
231 my @header_ids;
232
233 #
234 # Check for the presence of some frequently occurring naming schemes:
235 #
236 # >IPI:CON_Trypsin|SWISS-PROT:P00761|TRYP_PIG Trypsin - Sus scrofa (Pig).
237 # >IPI:CON_IPI00174775.2|TREMBL:Q32MB2;Q86Y46 Tax_Id=9606 Gene_Symbol=KRT73 Keratin-73
238 # >sp|Q42592|APXS_ARATH L-ascorbate peroxidase S, chloroplastic/mitochondrial;
239 # >jgi|Triad1|1|gw1.3.1.1
240 #
241 if ($line =~ m/^>((([^\s\n\r:;|]+)[:]([^\s\n\r:|]+)[|;])*([^\s\n\r:;|]+)[:]([^\s\n\r:|]+))[|;]?(\s+(.+))?/i) {
242
243 #
244 # One or more namespace prefixed IDs.
245 #
246 my $concatenated_namespace_prefixed_ids = $1;
247 $logger->debug('Found prefixed IDs in header: ' . $concatenated_namespace_prefixed_ids);
248
249 # database_namespace = $3 && $5;
250 # id = $4 && $6;
251 # description = $8;
252 my @namespace_prefixed_ids = split(/[|;]/, $concatenated_namespace_prefixed_ids);
253
254 foreach my $prefixed_id (@namespace_prefixed_ids) {
255
256 if ($prefixed_id =~ m/([^\s\n\r:;|]+:)?([^\s\n\r:|]+)/i) {
257
258 my $this_id = $2;
259
260 $logger->debug('Found ID: ' . $this_id);
261 push(@header_ids, $this_id);
262
263 } else {
264
265 $logger->warn(
266 'This should have been an optionally prefixed ID, '
267 . 'but failed to match the corresponding regex: '
268 . $prefixed_id);
269
270 }
271 }
272
273 } elsif ($line =~ m/^>((([^\s\n\r:;|]+)[|;])*([^\s\n\r:;|]+))[|;]?(\s+(.+))?/i) {
274
275 #
276 # One or more unprefixed IDs.
277 #
278 my $concatenated_ids = $1;
279 $logger->debug('Found unprefixed IDs in header: ' . $concatenated_ids);
280
281 # id = $3 && $4;
282 # description = $7;
283 my @unprefixed_ids = split(/[|;]/, $concatenated_ids);
284
285 foreach my $unprefixed_id (@unprefixed_ids) {
286
287 $logger->debug('Found ID: ' . $unprefixed_id);
288 push(@header_ids, $unprefixed_id);
289
290 }
291
292 } else {
293
294 #
295 # Something else.
296 #
297 # The FASTA header line can basically have any format,
298 # so this is probably one of the less frequent occurring annotation schemes.
299 # Therefore we try to see if the IDs we are looking for are present anywhere
300 # in the header line up until the first white space or new line.
301 # This may be tricky as we might match other annotation from other proteins
302 # like a description from a 'best' BLAST hit that contains one of the IDs we
303 # are looking for. Hence, in such a case this sequence is *not* the one of
304 # the IDs we looking for, but similar to that one at best.
305 #
306 if ($line =~ m/>([^\n\r\s]+)/) {
307
308 my $putative_id = $1;
309 $logger->debug('Found putative ID in header: ' . $putative_id);
310 push(@header_ids, $putative_id);
311
312 } else {
313 $logger->warn('Cannot identify IDs in this header: ' . $line);
314 }
315 }
316
317
318 if ($ignore_accession_version) {
319
320 for my $inx (0 .. $#header_ids) {
321
322 if ($header_ids[$inx] =~ m/([^\.]+)\.(\d+)/) {
323
324 my $this_unversioned_id = $1;
325 my $version_number = $2;
326 $logger->debug('Dropping version number (' . $version_number . ') for versioned ID: ' . $this_unversioned_id . '.');
327 $header_ids[$inx] = $this_unversioned_id;
328
329 }
330 }
331 }
332
333 foreach my $id (@header_ids) {
334 $logger->debug('Checking if ID ' . $id . ' is in the list of sequences to extract.');
335
336 if ($match_logic eq 'literal') {
337
338 if (${$wanted}{$id}) {
339 $logger->info('Literal bingo, preserving sequence with ID ' . $id);
340 $found = 1;
341 $extracted_seqs++;
342 last;
343 }
344
345 } elsif ($match_logic eq 'regex') {
346
347 foreach my $regex (keys(%{$wanted})) {
348
349 if ($id =~ m/$regex/) {
350 $logger->info('Regex bingo, preserving sequence with ID ' . $id);
351 $found = 1;
352 $extracted_seqs++;
353 last;
354 }
355 }
356 }
357 }
358 }
359 if ($found) {
360 print($path_to_fh $line);
361 }
362
363 }
364
365 close($path_from_fh);
366 close($path_to_fh);
367
368 return ($extracted_seqs);
369
370 }
371
372 sub _Usage {
373
374 print STDERR "\n"
375 . "extractSeqsFromFasta.pl:\n"
376 . " Extracts sequences from a multi-sequence FASTA file.\n" . "\n"
377 . "Usage:\n" . "\n"
378 . " extractSeqsFromFasta.pl options\n" . "\n"
379 . "Available options are:\n" . "\n"
380 . " -i [file] Input file in FASTA format.\n"
381 . " -o [file] Output file in FASTA format where the extracted files will be saved.\n"
382 . " -f [file] Filter file containing accession numbers or IDs that shoud be extracted from the input.\n"
383 . " (One accession/ID per line)\n"
384 . " -m [string] Match logic that defines how the accession numbers or IDs from the filter file will be.\n"
385 . " matched to those in the FASTA file. Supported logic types:\n"
386 . " literal for exact matching.\n"
387 . " regex for fuzzy matching using simple regular expressions (in Perl regex syntax).\n"
388 . " -u Use unversioned accession numbers for matching (only with -m literal).\n"
389 . " If the FASTA input file contains a versioned accession number like this IPI00189968.5,\n"
390 . " running this tool without -u (default) IPI00189968 or IPI00189968.2 will not match IPI00189968.5, \n"
391 . " but with -u IPI00189968 or IPI00189968.2 will match IPI00189968.5 and the sequence will be extracted.\n"
392 . " Hence this allows for less strict matching, but is less fuzzy than matching with regexes.\n"
393 . " -l [LEVEL] Log4perl log level. One of: ALL, TRACE, DEBUG, INFO (default), WARN, ERROR, FATAL or OFF.\n"
394 . "\n";
395 exit;
396
397 }