Source Code for Module Bio.AlignIO.EmbossIO

  1  # Copyright 2008-2010 by Peter Cock.  All rights reserved. 
  2  # 
  3  # This code is part of the Biopython distribution and governed by its 
  4  # license.  Please see the LICENSE file that should have been included 
  5  # as part of this package. 
  6  """ 
  7  Bio.AlignIO support for the "emboss" alignment output from EMBOSS tools. 
  8   
  9  You are expected to use this module via the Bio.AlignIO functions (or the 
 10  Bio.SeqIO functions if you want to work directly with the gapped sequences). 
 11   
 12  This module contains a parser for the EMBOSS pairs/simple file format, for 
 13  example from the alignret, water and needle tools. 
 14  """ 
 15   
 16  from Bio.Seq import Seq 
 17  from Bio.SeqRecord import SeqRecord 
 18  from Bio.Align import MultipleSeqAlignment 
 19  from Interfaces import AlignmentIterator, SequentialAlignmentWriter 
 20   
 21   
 22 -class EmbossWriter(SequentialAlignmentWriter): 
 23      """Emboss alignment writer (WORK IN PROGRESS). 
 24   
 25      Writes a simplfied version of the EMBOSS pairs/simple file format. 
 26      A lot of the information their tools record in their headers is not 
 27      available and is omitted. 
 28      """ 
 29   
 30 -    def write_header(self): 
 31          handle = self.handle 
 32          handle.write("########################################\n") 
 33          handle.write("# Program: Biopython\n") 
 34          try: 
 35              handle.write("# Report_file: %s\n" % handle.name) 
 36          except AttributeError: 
 37              pass 
 38          handle.write("########################################\n") 
 39   
 40 -    def write_footer(self): 
 41          handle = self.handle 
 42          handle.write("#---------------------------------------\n") 
 43          handle.write("#---------------------------------------\n") 
 44   
 45 -    def write_alignment(self, alignment): 
 46          """Use this to write (another) single alignment to an open file.""" 
 47          handle = self.handle 
 48          handle.write("#=======================================\n") 
 49          handle.write("#\n") 
 50          handle.write("# Aligned_sequences: %i\n" % len(alignment)) 
 51          for i, record in enumerate(alignment): 
 52              handle.write("# %i: %s\n" % (i+1, record.id)) 
 53          handle.write("#\n") 
 54          handle.write("# Length: %i\n" % alignment.get_alignment_length()) 
 55          handle.write("#\n") 
 56          handle.write("#=======================================\n") 
 57          handle.write("\n") 
 58          #... 
 59          assert False 
 60   
 61   
 62 -class EmbossIterator(AlignmentIterator): 
 63      """Emboss alignment iterator. 
 64   
 65      For reading the (pairwise) alignments from EMBOSS tools in what they 
 66      call the "pairs" and "simple" formats. 
 67      """ 
 68   
 69 -    def next(self): 
 70   
 71          handle = self.handle 
 72   
 73          try: 
 74              #Header we saved from when we were parsing 
 75              #the previous alignment. 
 76              line = self._header 
 77              del self._header 
 78          except AttributeError: 
 79              line = handle.readline() 
 80          if not line: 
 81              raise StopIteration 
 82   
 83          while line.rstrip() != "#=======================================": 
 84              line = handle.readline() 
 85              if not line: 
 86                  raise StopIteration 
 87   
 88          length_of_seqs = None 
 89          number_of_seqs = None 
 90          ids = [] 
 91          seqs = [] 
 92   
 93          while line[0] == "#": 
 94              #Read in the rest of this alignment header, 
 95              #try and discover the number of records expected 
 96              #and their length 
 97              parts = line[1:].split(":", 1) 
 98              key = parts[0].lower().strip() 
 99              if key == "aligned_sequences": 
100                  number_of_seqs = int(parts[1].strip()) 
101                  assert len(ids) == 0 
102                  # Should now expect the record identifiers... 
103                  for i in range(number_of_seqs): 
104                      line = handle.readline() 
105                      parts = line[1:].strip().split(":", 1) 
106                      assert i+1 == int(parts[0].strip()) 
107                      ids.append(parts[1].strip()) 
108                  assert len(ids) == number_of_seqs 
109              if key == "length": 
110                  length_of_seqs = int(parts[1].strip()) 
111   
112              #And read in another line... 
113              line = handle.readline() 
114   
115          if number_of_seqs is None: 
116              raise ValueError("Number of sequences missing!") 
117          if length_of_seqs is None: 
118              raise ValueError("Length of sequences missing!") 
119   
120          if self.records_per_alignment is not None \ 
121          and self.records_per_alignment != number_of_seqs: 
122              raise ValueError("Found %i records in this alignment, told to expect %i" 
123                               % (number_of_seqs, self.records_per_alignment)) 
124   
125          seqs = ["" for id in ids] 
126          seq_starts = [] 
127          index = 0 
128   
129          #Parse the seqs 
130          while line: 
131              if len(line) > 21: 
132                  id_start = line[:21].strip().split(None, 1) 
133                  seq_end = line[21:].strip().split(None, 1) 
134                  if len(id_start) == 2 and len(seq_end) == 2: 
135                      #identifier, seq start position, seq, seq end position 
136                      #(an aligned seq is broken up into multiple lines) 
137                      id, start = id_start 
138                      seq, end = seq_end 
139                      if start == end: 
140                          #Special case, either a single letter is present, 
141                          #or no letters at all. 
142                          if seq.replace("-", "") == "": 
143                              start = int(start) 
144                              end = int(end) 
145                          else: 
146                              start = int(start) - 1 
147                              end = int(end) 
148                      else: 
149                          assert seq.replace("-", "") != "" 
150                          start = int(start) - 1  # python counting 
151                          end = int(end) 
152   
153                      #The identifier is truncated... 
154                      assert 0 <= index and index < number_of_seqs, \ 
155                             "Expected index %i in range [0,%i)" \ 
156                             % (index, number_of_seqs) 
157                      assert id == ids[index] or id == ids[index][:len(id)] 
158   
159                      if len(seq_starts) == index: 
160                          #Record the start 
161                          seq_starts.append(start) 
162   
163                      #Check the start... 
164                      if start == end: 
165                          assert seq.replace("-", "") == "", line 
166                      else: 
167                          assert start - seq_starts[index] == len(seqs[index].replace("-","")), \ 
168                          "Found %i chars so far for sequence %i (%s, %s), line says start %i:\n%s" \ 
169                              % (len(seqs[index].replace("-","")), index, id, repr(seqs[index]), 
170                                 start, line) 
171   
172                      seqs[index] += seq 
173   
174                      #Check the end ... 
175                      assert end == seq_starts[index] + len(seqs[index].replace("-", "")), \ 
176                          "Found %i chars so far for sequence %i (%s, %s, start=%i), file says end %i:\n%s" \ 
177                              % (len(seqs[index].replace("-", "")), index, id, repr(seqs[index]), 
178                                 seq_starts[index], end, line) 
179   
180                      index += 1 
181                      if index >= number_of_seqs: 
182                          index = 0 
183                  else: 
184                      #just a start value, this is just alignment annotation (?) 
185                      #print "Skipping: " + line.rstrip() 
186                      pass 
187              elif line.strip() == "": 
188                  #Just a spacer? 
189                  pass 
190              else: 
191                  print line 
192                  assert False 
193   
194              line = handle.readline() 
195              if line.rstrip() == "#---------------------------------------" \ 
196              or line.rstrip() == "#=======================================": 
197                  #End of alignment 
198                  self._header = line 
199                  break 
200   
201          assert index == 0 
202   
203          if self.records_per_alignment is not None \ 
204          and self.records_per_alignment != len(ids): 
205              raise ValueError("Found %i records in this alignment, told to expect %i" 
206                               % (len(ids), self.records_per_alignment)) 
207   
208          records = [] 
209          for id, seq in zip(ids, seqs): 
210              if len(seq) != length_of_seqs: 
211                  #EMBOSS 2.9.0 is known to use spaces instead of minus signs 
212                  #for leading gaps, and thus fails to parse.  This old version 
213                  #is still used as of Dec 2008 behind the EBI SOAP webservice: 
214                  #http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl 
215                  raise ValueError("Error parsing alignment - sequences of " 
216                                   "different length? You could be using an " 
217                                   "old version of EMBOSS.") 
218              records.append(SeqRecord(Seq(seq, self.alphabet), 
219                                       id=id, description=id)) 
220          return MultipleSeqAlignment(records, self.alphabet) 
221   
222   
223  if __name__ == "__main__": 
224      print "Running a quick self-test" 
225   
226      #http://emboss.sourceforge.net/docs/themes/alnformats/align.simple 
227      simple_example = \ 
228  """######################################## 
229  # Program:  alignret 
230  # Rundate:  Wed Jan 16 17:16:13 2002 
231  # Report_file: stdout 
232  ######################################## 
233  #======================================= 
234  # 
235  # Aligned_sequences: 4 
236  # 1: IXI_234 
237  # 2: IXI_235 
238  # 3: IXI_236 
239  # 4: IXI_237 
240  # Matrix: EBLOSUM62 
241  # Gap_penalty: 10.0 
242  # Extend_penalty: 0.5 
243  # 
244  # Length: 131 
245  # Identity:      95/131 (72.5%) 
246  # Similarity:   127/131 (96.9%) 
247  # Gaps:          25/131 (19.1%) 
248  # Score: 100.0 
249  # 
250  # 
251  #======================================= 
252   
253  IXI_234            1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT     50 
254  IXI_235            1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT     41 
255  IXI_236            1 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQAT     48 
256  IXI_237            1 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQAT     45 
257                       |||||:|||||||||:::::::  |||||:||||:::::|||||:||||| 
258   
259  IXI_234           51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG    100 
260  IXI_235           42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG     81 
261  IXI_236           49 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--G     96 
262  IXI_237           46 GGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--G     93 
263                       ||:||||||||||||||||||||:::::::::::|||||||||||||  | 
264   
265  IXI_234          101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    131 
266  IXI_235           82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    112 
267  IXI_236           97 SRPPRFAPPLMSSCITSTTGPPPPAGDRSHE    127 
268  IXI_237           94 SRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE    124 
269                       |||:||||:|||||:|||||||::||||||| 
270   
271   
272  #--------------------------------------- 
273  #--------------------------------------- 
274   
275  """ 
276   
277      #http://emboss.sourceforge.net/docs/themes/alnformats/align.pair 
278      pair_example = \ 
279  """######################################## 
280  # Program:  water 
281  # Rundate:  Wed Jan 16 17:23:19 2002 
282  # Report_file: stdout 
283  ######################################## 
284  #======================================= 
285  # 
286  # Aligned_sequences: 2 
287  # 1: IXI_234 
288  # 2: IXI_235 
289  # Matrix: EBLOSUM62 
290  # Gap_penalty: 10.0 
291  # Extend_penalty: 0.5 
292  # 
293  # Length: 131 
294  # Identity:     112/131 (85.5%) 
295  # Similarity:   112/131 (85.5%) 
296  # Gaps:          19/131 (14.5%) 
297  # Score: 591.5 
298  # 
299  # 
300  #======================================= 
301   
302  IXI_234            1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT     50 
303                       |||||||||||||||         |||||||||||||||||||||||||| 
304  IXI_235            1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT     41 
305   
306  IXI_234           51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG    100 
307                       ||||||||||||||||||||||||          |||||||||||||||| 
308  IXI_235           42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG     81 
309   
310  IXI_234          101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    131 
311                       ||||||||||||||||||||||||||||||| 
312  IXI_235           82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE    112 
313   
314   
315  #--------------------------------------- 
316  #---------------------------------------        
317   
318   
319  """ 
320   
321      pair_example2 = \ 
322  """######################################## 
323  # Program: needle 
324  # Rundate: Sun 27 Apr 2007 17:20:35 
325  # Commandline: needle 
326  #    [-asequence] Spo0F.faa 
327  #    [-bsequence] paired_r.faa 
328  #    -sformat2 pearson 
329  # Align_format: srspair 
330  # Report_file: ref_rec .needle 
331  ######################################## 
332   
333  #======================================= 
334  # 
335  # Aligned_sequences: 2 
336  # 1: ref_rec 
337  # 2: gi|94968718|receiver 
338  # Matrix: EBLOSUM62 
339  # Gap_penalty: 10.0 
340  # Extend_penalty: 0.5 
341  # 
342  # Length: 124 
343  # Identity:      32/124 (25.8%) 
344  # Similarity:    64/124 (51.6%) 
345  # Gaps:          17/124 (13.7%) 
346  # Score: 112.0 
347  #  
348  # 
349  #======================================= 
350   
351  ref_rec            1 KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDL     46 
352                        :|:.||    :.|.|::|.:  :.|.....:|.:|.||:.:..:..|.: 
353  gi|94968718|r      1 -VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAVKLAGELHPRV     47 
354   
355  ref_rec           47 VLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALT     96 
356                       |::|..:|||.|::..|:::....:|.|:::|.:.|...::.:.|.||.. 
357  gi|94968718|r     48 VVMDCAMPGMSGMDATKQIRTQWPDIAVLMLTMHSEDTWVRLALEAGANG     97 
358   
359  ref_rec           97 HFAK-PFDIDEIRDAV--------    111 
360                       :..| ..|:|.|: ||         
361  gi|94968718|r     98 YILKSAIDLDLIQ-AVRRVANGET    120 
362   
363   
364  #======================================= 
365  # 
366  # Aligned_sequences: 2 
367  # 1: ref_rec 
368  # 2: gi|94968761|receiver 
369  # Matrix: EBLOSUM62 
370  # Gap_penalty: 10.0 
371  # Extend_penalty: 0.5 
372  # 
373  # Length: 119 
374  # Identity:      34/119 (28.6%) 
375  # Similarity:    58/119 (48.7%) 
376  # Gaps:           9/119 ( 7.6%) 
377  # Score: 154.0 
378  #  
379  # 
380  #======================================= 
381   
382  ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLD     50 
383                        ||||||:......|:..|...|::.....|.::||:|...:..||:|.| 
384  gi|94968761|r      1 -ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRALEIAKSKPFDLILSD     49 
385   
386  ref_rec           51 MKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAK    100 
387                       :.:||.||:.:|:.:|.......|::|:....::|..::..||||....| 
388  gi|94968761|r     50 VVMPGRDGLTLLEDLKTAGVQAPVVMMSGQAHIEMAVKATRLGALDFLEK     99 
389   
390  ref_rec          101 PFDIDEIRDAV--------    111 
391                       |...|::...|         
392  gi|94968761|r    100 PLSTDKLLLTVENALKLKR    118 
393   
394   
395  #======================================= 
396  # 
397  # Aligned_sequences: 2 
398  # 1: ref_rec 
399  # 2: gi|94967506|receiver 
400  # Matrix: EBLOSUM62 
401  # Gap_penalty: 10.0 
402  # Extend_penalty: 0.5 
403  # 
404  # Length: 120 
405  # Identity:      29/120 (24.2%) 
406  # Similarity:    53/120 (44.2%) 
407  # Gaps:           9/120 ( 7.5%) 
408  # Score: 121.0 
409  #  
410  # 
411  #======================================= 
412   
413  ref_rec            1 -KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLL     49 
414                        .|::|||..|..:.:..||.:.|:..........|.:.:.....||.:: 
415  gi|94967506|r      1 LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHPVDLAIV     50 
416   
417  ref_rec           50 DMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA     99 
418                       |:.:....|:|:|:|.:|....:..:|:|....|:|...|...||:.:.. 
419  gi|94967506|r     51 DVYLGSTTGVEVLRRCRVHRPKLYAVIITGQISLEMAARSIAEGAVDYIQ    100 
420   
421  ref_rec          100 KPFDIDEIRDAV--------    111 
422                       ||.|||.:.:..         
423  gi|94967506|r    101 KPIDIDALLNIAERALEHKE    120 
424   
425   
426  #======================================= 
427  # 
428  # Aligned_sequences: 2 
429  # 1: ref_rec 
430  # 2: gi|94970045|receiver 
431  # Matrix: EBLOSUM62 
432  # Gap_penalty: 10.0 
433  # Extend_penalty: 0.5 
434  # 
435  # Length: 118 
436  # Identity:      30/118 (25.4%) 
437  # Similarity:    64/118 (54.2%) 
438  # Gaps:           9/118 ( 7.6%) 
439  # Score: 126.0 
440  #  
441  # 
442  #======================================= 
443   
444  ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVL     48 
445                        :|:|:|:..:|....:.....||:...|.:|.:||.:.:|  ||.|::: 
446  gi|94970045|r      1 -VLLVEDEEALRAAAGDFLETRGYKIMTARDGTEALSMASKFAERIDVLI     49 
447   
448  ref_rec           49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF     98 
449                       .|:.:||:.|..:.:.:..|....:|:.|:.|.: :.:..:.|:.:.:.| 
450  gi|94970045|r     50 TDLVMPGISGRVLAQELVKIHPETKVMYMSGYDD-ETVMVNGEIDSSSAF     98 
451   
452  ref_rec           99 -AKPFDID----EIRDAV    111 
453                        .|||.:|    :||:.: 
454  gi|94970045|r     99 LRKPFRMDALSAKIREVL    116 
455   
456   
457  #======================================= 
458  # 
459  # Aligned_sequences: 2 
460  # 1: ref_rec 
461  # 2: gi|94970041|receiver 
462  # Matrix: EBLOSUM62 
463  # Gap_penalty: 10.0 
464  # Extend_penalty: 0.5 
465  # 
466  # Length: 125 
467  # Identity:      35/125 (28.0%) 
468  # Similarity:    70/125 (56.0%) 
469  # Gaps:          18/125 (14.4%) 
470  # Score: 156.5 
471  #  
472  # 
473  #======================================= 
474   
475  ref_rec            1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVL     48 
476                       .:|:|:|:.|:|.|:..:.:::||...:|.:|.:||:||  :.::.|::| 
477  gi|94970041|r      1 TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVRESTQKIDMLL     50 
478   
479  ref_rec           49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF     98 
480                       .|:.:.||.|.|:.:|:::...:::||.|:.|.:..:::.    |.||.. 
481  gi|94970041|r     51 SDVVLVGMSGRELSERLRIQMPSLKVIYMSGYTDDAIVRH----GVLTES     96 
482   
483  ref_rec           99 A----KPFDIDEIRDAV--------    111 
484                       |    |||..|.:...|         
485  gi|94970041|r     97 AEFLQKPFTSDSLLRKVRAVLQKRQ    121 
486   
487   
488  #--------------------------------------- 
489  #--------------------------------------- 
490   
491  """ 
492   
493      pair_example3 = """######################################## 
494  # Program: needle 
495  # Rundate: Mon 14 Jul 2008 11:45:42 
496  # Commandline: needle 
497  #    [-asequence] asis:TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGC 
498  #    [-bsequence] asis:TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTT 
499  #    -filter 
500  # Align_format: srspair 
501  # Report_file: stdout 
502  ######################################## 
503   
504  #======================================= 
505  # 
506  # Aligned_sequences: 2 
507  # 1: asis 
508  # 2: asis 
509  # Matrix: EDNAFULL 
510  # Gap_penalty: 10.0 
511  # Extend_penalty: 0.5 
512  # 
513  # Length: 667 
514  # Identity:     210/667 (31.5%) 
515  # Similarity:   210/667 (31.5%) 
516  # Gaps:         408/667 (61.2%) 
517  # Score: 561.0 
518  #  
519  # 
520  #======================================= 
521   
522  asis               1 TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAAT     50 
523                                                                          
524  asis               0 --------------------------------------------------      0 
525   
526  asis              51 AGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGA    100 
527                                                                          
528  asis               0 --------------------------------------------------      0 
529   
530  asis             101 CTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTG    150 
531                                                                          
532  asis               0 --------------------------------------------------      0 
533   
534  asis             151 GGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGA    200 
535                                   .||||||                                
536  asis               1 ------------TTATTAA-------------------------------      7 
537   
538  asis             201 TACTTATTGT------GTAGTAGCTCATTTTCATTATGTTCTTCGAATGG    244 
539                        .|||||.||      |||..|..||  ||||.||||.||.|    ||.| 
540  asis               8 -TCTTATGGTTTTGCCGTAAAATTTC--TTTCTTTATTTTTT----ATTG     50 
541   
542  asis             245 GAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT------GAAATTTTTAG    288 
543                                ||.|.|||||.|||.||||.||||      | ||||||||| 
544  asis              51 ---------TTAGGATTTTGTTGATTTTATTTTTCTCAAG-AATTTTTAG     90 
545   
546  asis             289 GTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGAATTTTA    331 
547                       ||.|.|||||||     ||||||||.|  ||.|      |||.|.||||| 
548  asis              91 GTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAAGTTTTA    134 
549   
550  asis             332 TTAGCCTTTGGTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTC    377 
551                       |||                 ||||||    .||||...||||..|||||. 
552  asis             135 TTA-----------------ATTTTTGGGGGGGGGGGGAGACGGGGTGTT    167 
553   
554  asis             378 GT-TGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATA--------    418 
555                       .| |||||||||||             ||  ||.||.||.||         
556  asis             168 ATCTGAATTAGTTT-------------TT--GGGAGTCTCTAGACATCTC    202 
557   
558  asis             419 -------------GGATCTACCTTTTATCTTTCTAAT--CTTTT----GT    449 
559                                    ||..||.||.|.|||..||||.||  |||||    |  
560  asis             203 ATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGG-    251 
561   
562  asis             450 TTTAGT-ATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTT    498 
563                          ||| |.|||     |||||||||.||| .||||||...||||||||| 
564  asis             252 ---AGTAAGAAT-----TTCGATTCAGCAA-CTTTAGTTCACAGTCTTTT    292 
565   
566  asis             499 TTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTT    548 
567                       ||||||||..| ||||||||                               
568  asis             293 TTTTTATTAAG-AAAGGTTT------------------------------    311 
569   
570  asis             549 TCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGT    598 
571                                                                          
572  asis             311 --------------------------------------------------    311 
573   
574  asis             599 GAAAGGGGGTTAATAGC    615 
575                                         
576  asis             311 -----------------    311 
577   
578   
579  #--------------------------------------- 
580  #---------------------------------------""" 
581   
582      from StringIO import StringIO 
583   
584      alignments = list(EmbossIterator(StringIO(pair_example))) 
585      assert len(alignments) == 1 
586      assert len(alignments[0]) == 2 
587      assert [r.id for r in alignments[0]] \ 
588             == ["IXI_234", "IXI_235"] 
589   
590      alignments = list(EmbossIterator(StringIO(simple_example))) 
591      assert len(alignments) == 1 
592      assert len(alignments[0]) == 4 
593      assert [r.id for r in alignments[0]] \ 
594             == ["IXI_234", "IXI_235", "IXI_236", "IXI_237"] 
595   
596      alignments = list(EmbossIterator(StringIO(pair_example + simple_example))) 
597      assert len(alignments) == 2 
598      assert len(alignments[0]) == 2 
599      assert len(alignments[1]) == 4 
600      assert [r.id for r in alignments[0]] \ 
601             == ["IXI_234", "IXI_235"] 
602      assert [r.id for r in alignments[1]] \ 
603             == ["IXI_234", "IXI_235", "IXI_236", "IXI_237"] 
604   
605      alignments = list(EmbossIterator(StringIO(pair_example2))) 
606      assert len(alignments) == 5 
607      assert len(alignments[0]) == 2 
608      assert [r.id for r in alignments[0]] \ 
609             == ["ref_rec", "gi|94968718|receiver"] 
610      assert [r.id for r in alignments[4]] \ 
611             == ["ref_rec", "gi|94970041|receiver"] 
612   
613      alignments = list(EmbossIterator(StringIO(pair_example3))) 
614      assert len(alignments) == 1 
615      assert len(alignments[0]) == 2 
616      assert [r.id for r in alignments[0]] \ 
617             == ["asis", "asis"] 
618   
619      print "Done" 
620