forked from biopython/biopython
/
Scanner.py
1662 lines (1517 loc) · 77.5 KB
/
Scanner.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
# Copyright 2007-2010 by Peter Cock. All rights reserved.
# Revisions copyright 2010 by Uri Laserson. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# This code is NOT intended for direct use. It provides a basic scanner
# (for use with a event consumer such as Bio.GenBank._FeatureConsumer)
# to parse a GenBank or EMBL file (with their shared INSDC feature table).
#
# It is used by Bio.GenBank to parse GenBank files
# It is also used by Bio.SeqIO to parse GenBank and EMBL files
#
# Feature Table Documentation:
# http://www.insdc.org/files/feature_table.html
# http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
# ftp://ftp.ncbi.nih.gov/genbank/docs/
#
# 17-MAR-2009: added wgs, wgs_scafld for GenBank whole genome shotgun master records.
# These are GenBank files that summarize the content of a project, and provide lists of
# scaffold and contig files in the project. These will be in annotations['wgs'] and
# annotations['wgs_scafld']. These GenBank files do not have sequences. See
# http://groups.google.com/group/bionet.molbio.genbank/browse_thread/thread/51fb88bf39e7dc36
# http://is.gd/nNgk
# for more details of this format, and an example.
# Added by Ying Huang & Iddo Friedberg
import warnings
import os
import re
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_alphabet, generic_protein
class InsdcScanner:
"""Basic functions for breaking up a GenBank/EMBL file into sub sections.
The International Nucleotide Sequence Database Collaboration (INSDC)
between the DDBJ, EMBL, and GenBank. These organisations all use the
same "Feature Table" layout in their plain text flat file formats.
However, the header and sequence sections of an EMBL file are very
different in layout to those produced by GenBank/DDBJ."""
#These constants get redefined with sensible values in the sub classes:
RECORD_START = "XXX" # "LOCUS " or "ID "
HEADER_WIDTH = 3 # 12 or 5
FEATURE_START_MARKERS = ["XXX***FEATURES***XXX"]
FEATURE_END_MARKERS = ["XXX***END FEATURES***XXX"]
FEATURE_QUALIFIER_INDENT = 0
FEATURE_QUALIFIER_SPACER = ""
SEQUENCE_HEADERS=["XXX"] #with right hand side spaces removed
def __init__(self, debug=0):
assert len(self.RECORD_START)==self.HEADER_WIDTH
for marker in self.SEQUENCE_HEADERS:
assert marker==marker.rstrip()
assert len(self.FEATURE_QUALIFIER_SPACER)==self.FEATURE_QUALIFIER_INDENT
self.debug = debug
self.line = None
def set_handle(self, handle):
self.handle = handle
self.line = ""
def find_start(self):
"""Read in lines until find the ID/LOCUS line, which is returned.
Any preamble (such as the header used by the NCBI on *.seq.gz archives)
will we ignored."""
while True:
if self.line:
line = self.line
self.line = ""
else:
line = self.handle.readline()
if not line:
if self.debug : print "End of file"
return None
if line[:self.HEADER_WIDTH]==self.RECORD_START:
if self.debug > 1: print "Found the start of a record:\n" + line
break
line = line.rstrip()
if line == "//":
if self.debug > 1: print "Skipping // marking end of last record"
elif line == "":
if self.debug > 1: print "Skipping blank line before record"
else:
#Ignore any header before the first ID/LOCUS line.
if self.debug > 1:
print "Skipping header line before record:\n" + line
self.line = line
return line
def parse_header(self):
"""Return list of strings making up the header
New line characters are removed.
Assumes you have just read in the ID/LOCUS line.
"""
assert self.line[:self.HEADER_WIDTH]==self.RECORD_START, \
"Not at start of record"
header_lines = []
while True:
line = self.handle.readline()
if not line:
raise ValueError("Premature end of line during sequence data")
line = line.rstrip()
if line in self.FEATURE_START_MARKERS:
if self.debug : print "Found header table"
break
#if line[:self.HEADER_WIDTH]==self.FEATURE_START_MARKER[:self.HEADER_WIDTH]:
# if self.debug : print "Found header table (?)"
# break
if line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
if self.debug : print "Found start of sequence"
break
if line == "//":
raise ValueError("Premature end of sequence data marker '//' found")
header_lines.append(line)
self.line = line
return header_lines
def parse_features(self, skip=False):
"""Return list of tuples for the features (if present)
Each feature is returned as a tuple (key, location, qualifiers)
where key and location are strings (e.g. "CDS" and
"complement(join(490883..490885,1..879))") while qualifiers
is a list of two string tuples (feature qualifier keys and values).
Assumes you have already read to the start of the features table.
"""
if self.line.rstrip() not in self.FEATURE_START_MARKERS:
if self.debug : print "Didn't find any feature table"
return []
while self.line.rstrip() in self.FEATURE_START_MARKERS:
self.line = self.handle.readline()
features = []
line = self.line
while True:
if not line:
raise ValueError("Premature end of line during features table")
if line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
if self.debug : print "Found start of sequence"
break
line = line.rstrip()
if line == "//":
raise ValueError("Premature end of features table, marker '//' found")
if line in self.FEATURE_END_MARKERS:
if self.debug : print "Found end of features"
line = self.handle.readline()
break
if line[2:self.FEATURE_QUALIFIER_INDENT].strip() == "":
raise ValueError("Expected a feature qualifier in line '%s'" % line)
if skip:
line = self.handle.readline()
while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER:
line = self.handle.readline()
else:
#Build up a list of the lines making up this feature:
if line[self.FEATURE_QUALIFIER_INDENT]!=" " \
and " " in line[self.FEATURE_QUALIFIER_INDENT:]:
#The feature table design enforces a length limit on the feature keys.
#Some third party files (e.g. IGMT's EMBL like files) solve this by
#over indenting the location and qualifiers.
feature_key, line = line[2:].strip().split(None,1)
feature_lines = [line]
import warnings
warnings.warn("Overindented %s feature?" % feature_key)
else:
feature_key = line[2:self.FEATURE_QUALIFIER_INDENT].strip()
feature_lines = [line[self.FEATURE_QUALIFIER_INDENT:]]
line = self.handle.readline()
while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER \
or line.rstrip() == "" : # cope with blank lines in the midst of a feature
#Use strip to remove any harmless trailing white space AND and leading
#white space (e.g. out of spec files with too much intentation)
feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT:].strip())
line = self.handle.readline()
features.append(self.parse_feature(feature_key, feature_lines))
self.line = line
return features
def parse_feature(self, feature_key, lines):
"""Expects a feature as a list of strings, returns a tuple (key, location, qualifiers)
For example given this GenBank feature:
CDS complement(join(490883..490885,1..879))
/locus_tag="NEQ001"
/note="conserved hypothetical [Methanococcus jannaschii];
COG1583:Uncharacterized ACR; IPR001472:Bipartite nuclear
localization signal; IPR002743: Protein of unknown
function DUF57"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="NP_963295.1"
/db_xref="GI:41614797"
/db_xref="GeneID:2732620"
/translation="MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK
EKYFNFTLIPKKDIIENKRYYLIISSPDKRFIEVLHNKIKDLDIITIGLAQFQLRKTK
KFDPKLRFPWVTITPIVLREGKIVILKGDKYYKVFVKRLEELKKYNLIKKKEPILEEP
IEISLNQIKDGWKIIDVKDRYYDFRNKSFSAFSNWLRDLKEQSLRKYNNFCGKNFYFE
EAIFEGFTFYKTVSIRIRINRGEAVYIGTLWKELNVYRKLDKEEREFYKFLYDCGLGS
LNSMGFGFVNTKKNSAR"
Then should give input key="CDS" and the rest of the data as a list of strings
lines=["complement(join(490883..490885,1..879))", ..., "LNSMGFGFVNTKKNSAR"]
where the leading spaces and trailing newlines have been removed.
Returns tuple containing: (key as string, location string, qualifiers as list)
as follows for this example:
key = "CDS", string
location = "complement(join(490883..490885,1..879))", string
qualifiers = list of string tuples:
[('locus_tag', '"NEQ001"'),
('note', '"conserved hypothetical [Methanococcus jannaschii];\nCOG1583:..."'),
('codon_start', '1'),
('transl_table', '11'),
('product', '"hypothetical protein"'),
('protein_id', '"NP_963295.1"'),
('db_xref', '"GI:41614797"'),
('db_xref', '"GeneID:2732620"'),
('translation', '"MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK\nEKYFNFT..."')]
In the above example, the "note" and "translation" were edited for compactness,
and they would contain multiple new line characters (displayed above as \n)
If a qualifier is quoted (in this case, everything except codon_start and
transl_table) then the quotes are NOT removed.
Note that no whitespace is removed.
"""
#Skip any blank lines
iterator = iter(filter(None, lines))
try:
line = iterator.next()
feature_location = line.strip()
while feature_location[-1:]==",":
#Multiline location, still more to come!
feature_location += iterator.next().strip()
qualifiers=[]
for line in iterator:
if line[0]=="/":
#New qualifier
i = line.find("=")
key = line[1:i] #does not work if i==-1
value = line[i+1:] #we ignore 'value' if i==-1
if i==-1:
#Qualifier with no key, e.g. /pseudo
key = line[1:]
qualifiers.append((key,None))
elif value[0]=='"':
#Quoted...
if value[-1]!='"' or value!='"':
#No closing quote on the first line...
while value[-1] != '"':
value += "\n" + iterator.next()
else:
#One single line (quoted)
assert value == '"'
if self.debug : print "Quoted line %s:%s" % (key, value)
#DO NOT remove the quotes...
qualifiers.append((key,value))
else:
#Unquoted
#if debug : print "Unquoted line %s:%s" % (key,value)
qualifiers.append((key,value))
else:
#Unquoted continuation
assert len(qualifiers) > 0
assert key==qualifiers[-1][0]
#if debug : print "Unquoted Cont %s:%s" % (key, line)
qualifiers[-1] = (key, qualifiers[-1][1] + "\n" + line)
return (feature_key, feature_location, qualifiers)
except StopIteration:
#Bummer
raise ValueError("Problem with '%s' feature:\n%s" \
% (feature_key, "\n".join(lines)))
def parse_footer(self):
"""returns a tuple containing a list of any misc strings, and the sequence"""
#This is a basic bit of code to scan and discard the sequence,
#which was useful when developing the sub classes.
if self.line in self.FEATURE_END_MARKERS:
while self.line[:self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS:
self.line = self.handle.readline()
if not self.line:
raise ValueError("Premature end of file")
self.line = self.line.rstrip()
assert self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS, \
"Not at start of sequence"
while True:
line = self.handle.readline()
if not line : raise ValueError("Premature end of line during sequence data")
line = line.rstrip()
if line == "//" : break
self.line = line
return ([],"") #Dummy values!
def _feed_first_line(self, consumer, line):
"""Handle the LOCUS/ID line, passing data to the comsumer
This should be implemented by the EMBL / GenBank specific subclass
Used by the parse_records() and parse() methods.
"""
pass
def _feed_header_lines(self, consumer, lines):
"""Handle the header lines (list of strings), passing data to the comsumer
This should be implemented by the EMBL / GenBank specific subclass
Used by the parse_records() and parse() methods.
"""
pass
def _feed_feature_table(self, consumer, feature_tuples):
"""Handle the feature table (list of tuples), passing data to the comsumer
Used by the parse_records() and parse() methods.
"""
consumer.start_feature_table()
for feature_key, location_string, qualifiers in feature_tuples:
consumer.feature_key(feature_key)
consumer.location(location_string)
for q_key, q_value in qualifiers:
consumer.feature_qualifier_name([q_key])
if q_value is not None:
consumer.feature_qualifier_description(q_value.replace("\n"," "))
def _feed_misc_lines(self, consumer, lines):
"""Handle any lines between features and sequence (list of strings), passing data to the consumer
This should be implemented by the EMBL / GenBank specific subclass
Used by the parse_records() and parse() methods.
"""
pass
def feed(self, handle, consumer, do_features=True):
"""Feed a set of data into the consumer.
This method is intended for use with the "old" code in Bio.GenBank
Arguments:
handle - A handle with the information to parse.
consumer - The consumer that should be informed of events.
do_features - Boolean, should the features be parsed?
Skipping the features can be much faster.
Return values:
true - Passed a record
false - Did not find a record
"""
#Should work with both EMBL and GenBank files provided the
#equivalent Bio.GenBank._FeatureConsumer methods are called...
self.set_handle(handle)
if not self.find_start():
#Could not find (another) record
consumer.data=None
return False
#We use the above class methods to parse the file into a simplified format.
#The first line, header lines and any misc lines after the features will be
#dealt with by GenBank / EMBL specific derived classes.
#First line and header:
self._feed_first_line(consumer, self.line)
self._feed_header_lines(consumer, self.parse_header())
#Features (common to both EMBL and GenBank):
if do_features:
self._feed_feature_table(consumer, self.parse_features(skip=False))
else:
self.parse_features(skip=True) # ignore the data
#Footer and sequence
misc_lines, sequence_string = self.parse_footer()
self._feed_misc_lines(consumer, misc_lines)
consumer.sequence(sequence_string)
#Calls to consumer.base_number() do nothing anyway
consumer.record_end("//")
assert self.line == "//"
#And we are done
return True
def parse(self, handle, do_features=True):
"""Returns a SeqRecord (with SeqFeatures if do_features=True)
See also the method parse_records() for use on multi-record files.
"""
from Bio.GenBank import _FeatureConsumer
from Bio.GenBank.utils import FeatureValueCleaner
consumer = _FeatureConsumer(use_fuzziness = 1,
feature_cleaner = FeatureValueCleaner())
if self.feed(handle, consumer, do_features):
return consumer.data
else:
return None
def parse_records(self, handle, do_features=True):
"""Returns a SeqRecord object iterator
Each record (from the ID/LOCUS line to the // line) becomes a SeqRecord
The SeqRecord objects include SeqFeatures if do_features=True
This method is intended for use in Bio.SeqIO
"""
#This is a generator function
while True:
record = self.parse(handle, do_features)
if record is None : break
assert record.id is not None
assert record.name != "<unknown name>"
assert record.description != "<unknown description>"
yield record
def parse_cds_features(self, handle,
alphabet=generic_protein,
tags2id=('protein_id','locus_tag','product')):
"""Returns SeqRecord object iterator
Each CDS feature becomes a SeqRecord.
alphabet - Used for any sequence found in a translation field.
tags2id - Tupple of three strings, the feature keys to use
for the record id, name and description,
This method is intended for use in Bio.SeqIO
"""
self.set_handle(handle)
while self.find_start():
#Got an EMBL or GenBank record...
self.parse_header() # ignore header lines!
feature_tuples = self.parse_features()
#self.parse_footer() # ignore footer lines!
while True:
line = self.handle.readline()
if not line : break
if line[:2]=="//" : break
self.line = line.rstrip()
#Now go though those features...
for key, location_string, qualifiers in feature_tuples:
if key=="CDS":
#Create SeqRecord
#================
#SeqRecord objects cannot be created with annotations, they
#must be added afterwards. So create an empty record and
#then populate it:
record = SeqRecord(seq=None)
annotations = record.annotations
#Should we add a location object to the annotations?
#I *think* that only makes sense for SeqFeatures with their
#sub features...
annotations['raw_location'] = location_string.replace(' ','')
for (qualifier_name, qualifier_data) in qualifiers:
if qualifier_data is not None \
and qualifier_data[0]=='"' and qualifier_data[-1]=='"':
#Remove quotes
qualifier_data = qualifier_data[1:-1]
#Append the data to the annotation qualifier...
if qualifier_name == "translation":
assert record.seq is None, "Multiple translations!"
record.seq = Seq(qualifier_data.replace("\n",""), alphabet)
elif qualifier_name == "db_xref":
#its a list, possibly empty. Its safe to extend
record.dbxrefs.append(qualifier_data)
else:
if qualifier_data is not None:
qualifier_data = qualifier_data.replace("\n"," ").replace(" "," ")
try:
annotations[qualifier_name] += " " + qualifier_data
except KeyError:
#Not an addition to existing data, its the first bit
annotations[qualifier_name]= qualifier_data
#Fill in the ID, Name, Description
#=================================
try:
record.id = annotations[tags2id[0]]
except KeyError:
pass
try:
record.name = annotations[tags2id[1]]
except KeyError:
pass
try:
record.description = annotations[tags2id[2]]
except KeyError:
pass
yield record
class EmblScanner(InsdcScanner):
"""For extracting chunks of information in EMBL files"""
RECORD_START = "ID "
HEADER_WIDTH = 5
FEATURE_START_MARKERS = ["FH Key Location/Qualifiers","FH"]
FEATURE_END_MARKERS = ["XX"] #XX can also mark the end of many things!
FEATURE_QUALIFIER_INDENT = 21
FEATURE_QUALIFIER_SPACER = "FT" + " " * (FEATURE_QUALIFIER_INDENT-2)
SEQUENCE_HEADERS=["SQ", "CO"] #Remove trailing spaces
def parse_footer(self):
"""returns a tuple containing a list of any misc strings, and the sequence"""
assert self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS, \
"Eh? '%s'" % self.line
#Note that the SQ line can be split into several lines...
misc_lines = []
while self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
misc_lines.append(self.line)
self.line = self.handle.readline()
if not self.line:
raise ValueError("Premature end of file")
self.line = self.line.rstrip()
assert self.line[:self.HEADER_WIDTH] == " " * self.HEADER_WIDTH \
or self.line.strip() == '//', repr(self.line)
seq_lines = []
line = self.line
while True:
if not line:
raise ValueError("Premature end of file in sequence data")
line = line.strip()
if not line:
raise ValueError("Blank line in sequence data")
if line=='//':
break
assert self.line[:self.HEADER_WIDTH] == " " * self.HEADER_WIDTH, \
repr(self.line)
seq_lines.append("".join(line.split()[:-1]))
line = self.handle.readline()
self.line = line
return (misc_lines, "".join(seq_lines))
def _feed_first_line(self, consumer, line):
assert line[:self.HEADER_WIDTH].rstrip() == "ID"
if line[self.HEADER_WIDTH:].count(";") == 6:
#Looks like the semi colon separated style introduced in 2006
self._feed_first_line_new(consumer, line)
elif line[self.HEADER_WIDTH:].count(";") == 3:
#Looks like the pre 2006 style
self._feed_first_line_old(consumer, line)
else:
raise ValueError('Did not recognise the ID line layout:\n' + line)
def _feed_first_line_old(self, consumer, line):
#Expects an ID line in the style before 2006, e.g.
#ID SC10H5 standard; DNA; PRO; 4870 BP.
#ID BSUB9999 standard; circular DNA; PRO; 4214630 BP.
assert line[:self.HEADER_WIDTH].rstrip() == "ID"
fields = [line[self.HEADER_WIDTH:].split(None,1)[0]]
fields.extend(line[self.HEADER_WIDTH:].split(None,1)[1].split(";"))
fields = [entry.strip() for entry in fields]
"""
The tokens represent:
0. Primary accession number
(space sep)
1. ??? (e.g. standard)
(semi-colon)
2. Topology and/or Molecule type (e.g. 'circular DNA' or 'DNA')
3. Taxonomic division (e.g. 'PRO')
4. Sequence length (e.g. '4639675 BP.')
"""
consumer.locus(fields[0]) #Should we also call the accession consumer?
consumer.residue_type(fields[2])
consumer.data_file_division(fields[3])
self._feed_seq_length(consumer, fields[4])
def _feed_first_line_new(self, consumer, line):
#Expects an ID line in the style introduced in 2006, e.g.
#ID X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
#ID CD789012; SV 4; linear; genomic DNA; HTG; MAM; 500 BP.
assert line[:self.HEADER_WIDTH].rstrip() == "ID"
fields = [data.strip() for data in line[self.HEADER_WIDTH:].strip().split(";")]
assert len(fields) == 7
"""
The tokens represent:
0. Primary accession number
1. Sequence version number
2. Topology: 'circular' or 'linear'
3. Molecule type (e.g. 'genomic DNA')
4. Data class (e.g. 'STD')
5. Taxonomic division (e.g. 'PRO')
6. Sequence length (e.g. '4639675 BP.')
"""
consumer.locus(fields[0])
#Call the accession consumer now, to make sure we record
#something as the record.id, in case there is no AC line
consumer.accession(fields[0])
#TODO - How to deal with the version field? At the moment the consumer
#will try and use this for the ID which isn't ideal for EMBL files.
version_parts = fields[1].split()
if len(version_parts)==2 \
and version_parts[0]=="SV" \
and version_parts[1].isdigit():
consumer.version_suffix(version_parts[1])
#Based on how the old GenBank parser worked, merge these two:
consumer.residue_type(" ".join(fields[2:4])) #TODO - Store as two fields?
#consumer.xxx(fields[4]) #TODO - What should we do with the data class?
consumer.data_file_division(fields[5])
self._feed_seq_length(consumer, fields[6])
def _feed_seq_length(self, consumer, text):
length_parts = text.split()
assert len(length_parts) == 2
assert length_parts[1].upper() in ["BP", "BP."]
consumer.size(length_parts[0])
def _feed_header_lines(self, consumer, lines):
EMBL_INDENT = self.HEADER_WIDTH
EMBL_SPACER = " " * EMBL_INDENT
consumer_dict = {
'AC' : 'accession',
'SV' : 'version', # SV line removed in June 2006, now part of ID line
'DE' : 'definition',
#'RN' : 'reference_num',
#'RC' : reference comment... TODO
#'RP' : 'reference_bases',
#'RX' : reference cross reference... DOI or Pubmed
'RG' : 'consrtm', #optional consortium
#'RA' : 'authors',
#'RT' : 'title',
'RL' : 'journal',
'OS' : 'organism',
'OC' : 'taxonomy',
#'DR' : data reference?
'CC' : 'comment',
#'XX' : splitter
}
#We have to handle the following specially:
#RX (depending on reference type...)
lines = filter(None,lines)
line_iter = iter(lines)
try:
while True:
try:
line = line_iter.next()
except StopIteration:
break
if not line : break
line_type = line[:EMBL_INDENT].strip()
data = line[EMBL_INDENT:].strip()
if line_type == 'XX':
pass
elif line_type == 'RN':
# Reformat reference numbers for the GenBank based consumer
# e.g. '[1]' becomes '1'
if data[0] == "[" and data[-1] == "]" : data = data[1:-1]
consumer.reference_num(data)
elif line_type == 'RP':
# Reformat reference numbers for the GenBank based consumer
# e.g. '1-4639675' becomes '(bases 1 to 4639675)'
# and '160-550, 904-1055' becomes '(bases 160 to 550; 904 to 1055)'
parts = [bases.replace("-"," to ").strip() for bases in data.split(",")]
consumer.reference_bases("(bases %s)" % "; ".join(parts))
elif line_type == 'RT':
#Remove the enclosing quotes and trailing semi colon.
#Note the title can be split over multiple lines.
if data.startswith('"'):
data = data[1:]
if data.endswith('";'):
data = data[:-2]
consumer.title(data)
elif line_type == 'RX':
# EMBL support three reference types at the moment:
# - PUBMED PUBMED bibliographic database (NLM)
# - DOI Digital Object Identifier (International DOI Foundation)
# - AGRICOLA US National Agriculture Library (NAL) of the US Department
# of Agriculture (USDA)
#
# Format:
# RX resource_identifier; identifier.
#
# e.g.
# RX DOI; 10.1016/0024-3205(83)90010-3.
# RX PUBMED; 264242.
#
# Currently our reference object only supports PUBMED and MEDLINE
# (as these were in GenBank files?).
key, value = data.split(";",1)
if value.endswith(".") : value = value[:-1]
value = value.strip()
if key == "PUBMED":
consumer.pubmed_id(value)
#TODO - Handle other reference types (here and in BioSQL bindings)
elif line_type == 'CC':
# Have to pass a list of strings for this one (not just a string)
consumer.comment([data])
elif line_type == 'DR':
# Database Cross-reference, format:
# DR database_identifier; primary_identifier; secondary_identifier.
#
# e.g.
# DR MGI; 98599; Tcrb-V4.
#
# TODO - Data reference...
# How should we store the secondary identifier (if present)? Ignore it?
pass
elif line_type == 'RA':
# Remove trailing ; at end of authors list
consumer.authors(data.rstrip(";"))
elif line_type == 'PR':
# Remove trailing ; at end of the project reference
# In GenBank files this corresponds to the old PROJECT
# line which is being replaced with the DBLINK line.
consumer.project(data.rstrip(";"))
elif line_type in consumer_dict:
#Its a semi-automatic entry!
getattr(consumer, consumer_dict[line_type])(data)
else:
if self.debug:
print "Ignoring EMBL header line:\n%s" % line
except StopIteration:
raise ValueError("Problem with header")
def _feed_misc_lines(self, consumer, lines):
#TODO - Should we do something with the information on the SQ line(s)?
lines.append("")
line_iter = iter(lines)
try:
for line in line_iter:
if line.startswith("CO "):
line = line[5:].strip()
contig_location = line
while True:
line = line_iter.next()
if not line:
break
elif line.startswith("CO "):
#Don't need to preseve the whitespace here.
contig_location += line[5:].strip()
else:
raise ValueError('Expected CO (contig) continuation line, got:\n' + line)
consumer.contig_location(contig_location)
return
except StopIteration:
raise ValueError("Problem in misc lines before sequence")
class _ImgtScanner(EmblScanner):
"""For extracting chunks of information in IMGT (EMBL like) files (PRIVATE).
IMGT files are like EMBL files but in order to allow longer feature types
the features should be indented by 25 characters not 21 characters. In
practice the IMGT flat files tend to use either 21 or 25 characters, so we
must cope with both.
This is private to encourage use of Bio.SeqIO rather than Bio.GenBank.
"""
FEATURE_START_MARKERS = ["FH Key Location/Qualifiers",
"FH Key Location/Qualifiers (from EMBL)",
"FH Key Location/Qualifiers",
"FH"]
def parse_features(self, skip=False):
"""Return list of tuples for the features (if present)
Each feature is returned as a tuple (key, location, qualifiers)
where key and location are strings (e.g. "CDS" and
"complement(join(490883..490885,1..879))") while qualifiers
is a list of two string tuples (feature qualifier keys and values).
Assumes you have already read to the start of the features table.
"""
if self.line.rstrip() not in self.FEATURE_START_MARKERS:
if self.debug : print "Didn't find any feature table"
return []
while self.line.rstrip() in self.FEATURE_START_MARKERS:
self.line = self.handle.readline()
bad_position_re = re.compile(r'([0-9]+)>{1}')
features = []
line = self.line
while True:
if not line:
raise ValueError("Premature end of line during features table")
if line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
if self.debug : print "Found start of sequence"
break
line = line.rstrip()
if line == "//":
raise ValueError("Premature end of features table, marker '//' found")
if line in self.FEATURE_END_MARKERS:
if self.debug : print "Found end of features"
line = self.handle.readline()
break
if line[2:self.FEATURE_QUALIFIER_INDENT].strip() == "":
raise ValueError("Expected a feature qualifier in line '%s'" % line)
if skip:
line = self.handle.readline()
while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER:
line = self.handle.readline()
else:
assert line[:2] == "FT"
try:
feature_key, location_start = line[2:].strip().split()
except ValueError:
#e.g. "FT TRANSMEMBRANE-REGION2163..2240\n"
#Assume indent of 25 as per IMGT spec, with the location
#start in column 26 (one-based).
feature_key = line[2:25].strip()
location_start = line[25:].strip()
if location_start == "1.":
#Nasty hack for common IMGT bug, probably should be 1..end
#if we had the sequence length information here.
location_start = "1"
if ">" in location_start:
#Nasty hack for common IMGT bug, should be >123 not 123>
#in a location string.
location_start = bad_position_re.sub(r'>\1',location_start)
feature_lines = [location_start]
line = self.handle.readline()
while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER \
or line.rstrip() == "" : # cope with blank lines in the midst of a feature
#Use strip to remove any harmless trailing white space AND and leading
#white space (copes with 21 or 26 indents and orther variants)
assert line[:2] == "FT"
feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT:].strip())
line = self.handle.readline()
features.append(self.parse_feature(feature_key, feature_lines))
self.line = line
return features
class GenBankScanner(InsdcScanner):
"""For extracting chunks of information in GenBank files"""
RECORD_START = "LOCUS "
HEADER_WIDTH = 12
FEATURE_START_MARKERS = ["FEATURES Location/Qualifiers","FEATURES"]
FEATURE_END_MARKERS = []
FEATURE_QUALIFIER_INDENT = 21
FEATURE_QUALIFIER_SPACER = " " * FEATURE_QUALIFIER_INDENT
SEQUENCE_HEADERS=["CONTIG", "ORIGIN", "BASE COUNT", "WGS"] # trailing spaces removed
def parse_footer(self):
"""returns a tuple containing a list of any misc strings, and the sequence"""
assert self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS, \
"Eh? '%s'" % self.line
misc_lines = []
while self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS \
or self.line[:self.HEADER_WIDTH] == " "*self.HEADER_WIDTH \
or "WGS" == self.line[:3]:
misc_lines.append(self.line.rstrip())
self.line = self.handle.readline()
if not self.line:
raise ValueError("Premature end of file")
self.line = self.line
assert self.line[:self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS, \
"Eh? '%s'" % self.line
#Now just consume the sequence lines until reach the // marker
#or a CONTIG line
seq_lines = []
line = self.line
while True:
if not line:
raise ValueError("Premature end of file in sequence data")
line = line.rstrip()
if not line:
import warnings
warnings.warn("Blank line in sequence data")
line = self.handle.readline()
continue
if line=='//':
break
if line.find('CONTIG')==0:
break
if len(line) > 9 and line[9:10]!=' ':
raise ValueError("Sequence line mal-formed, '%s'" % line)
seq_lines.append(line[10:].replace(" ",""))
line = self.handle.readline()
self.line = line
#Seq("".join(seq_lines), self.alphabet)
return (misc_lines,"".join(seq_lines))
def _feed_first_line(self, consumer, line):
#####################################
# LOCUS line #
#####################################
GENBANK_INDENT = self.HEADER_WIDTH
GENBANK_SPACER = " "*GENBANK_INDENT
assert line[0:GENBANK_INDENT] == 'LOCUS ', \
'LOCUS line does not start correctly:\n' + line
#Have to break up the locus line, and handle the different bits of it.
#There are at least two different versions of the locus line...
if line[29:33] in [' bp ', ' aa ',' rc ']:
#Old...
#
# Positions Contents
# --------- --------
# 00:06 LOCUS
# 06:12 spaces
# 12:?? Locus name
# ??:?? space
# ??:29 Length of sequence, right-justified
# 29:33 space, bp, space
# 33:41 strand type
# 41:42 space
# 42:51 Blank (implies linear), linear or circular
# 51:52 space
# 52:55 The division code (e.g. BCT, VRL, INV)
# 55:62 space
# 62:73 Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
#
assert line[29:33] in [' bp ', ' aa ',' rc '] , \
'LOCUS line does not contain size units at expected position:\n' + line
assert line[41:42] == ' ', \
'LOCUS line does not contain space at position 42:\n' + line
assert line[42:51].strip() in ['','linear','circular'], \
'LOCUS line does not contain valid entry (linear, circular, ...):\n' + line
assert line[51:52] == ' ', \
'LOCUS line does not contain space at position 52:\n' + line
assert line[55:62] == ' ', \
'LOCUS line does not contain spaces from position 56 to 62:\n' + line
if line[62:73].strip():
assert line[64:65] == '-', \
'LOCUS line does not contain - at position 65 in date:\n' + line
assert line[68:69] == '-', \
'LOCUS line does not contain - at position 69 in date:\n' + line
name_and_length_str = line[GENBANK_INDENT:29]
while name_and_length_str.find(' ')!=-1:
name_and_length_str = name_and_length_str.replace(' ',' ')
name_and_length = name_and_length_str.split(' ')
assert len(name_and_length)<=2, \
'Cannot parse the name and length in the LOCUS line:\n' + line
assert len(name_and_length)!=1, \
'Name and length collide in the LOCUS line:\n' + line
#Should be possible to split them based on position, if
#a clear definition of the standard exists THAT AGREES with
#existing files.
consumer.locus(name_and_length[0])
consumer.size(name_and_length[1])
#consumer.residue_type(line[33:41].strip())
if line[33:51].strip() == "" and line[29:33] == ' aa ':
#Amino acids -> protein (even if there is no residue type given)
#We want to use a protein alphabet in this case, rather than a
#generic one. Not sure if this is the best way to achieve this,
#but it works because the scanner checks for this:
consumer.residue_type("PROTEIN")
else:
consumer.residue_type(line[33:51].strip())
consumer.data_file_division(line[52:55])
if line[62:73].strip():
consumer.date(line[62:73])
elif line[40:44] in [' bp ', ' aa ',' rc ']:
#New...
#
# Positions Contents
# --------- --------
# 00:06 LOCUS