1
2
3
4
5
6 """
7 Note
8 ====
9 In TREE_PUZZLE (Schmidt et al. 2003) and PHYML (Guindon and Gascuel 2003)
10 a dot/period (".") in a sequence is interpreted as meaning the same
11 character as in the first sequence. The PHYLIP 3.6 documentation says:
12
13 "a period was also previously allowed but it is no longer allowed,
14 because it sometimes is used in different senses in other programs"
15
16 At the time of writing, we do nothing special with a dot/period.
17 """
18
19 from Bio.Alphabet import single_letter_alphabet
20 from sets import Set
21
22 from Bio.Align.Generic import Alignment
23 from Interfaces import AlignmentIterator, SequentialAlignmentWriter
24
26 """Phylip alignment writer."""
28 """Use this to write (another) single alignment to an open file.
29
30 This code will write interlaced alignments (when the sequences are
31 longer than 50 characters).
32
33 Note that record identifiers are strictly truncated at 10 characters.
34
35 For more information on the file format, please see:
36 http://evolution.genetics.washington.edu/phylip/doc/sequence.html
37 http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
38 """
39 truncate=10
40 records = alignment.get_all_seqs()
41 handle = self.handle
42
43 if len(records)==0 :
44 raise ValueError("Must have at least one sequence")
45 length_of_seqs = alignment.get_alignment_length()
46 for record in records :
47 if length_of_seqs <> len(record.seq) :
48 raise ValueError("Sequences must all be the same length")
49 if length_of_seqs <= 0 :
50 raise ValueError("Non-empty sequences are required")
51
52 if len(records) > len(Set([r.id[:truncate] for r in records])) :
53 raise ValueError("Repeated identifier, possibly due to truncation")
54
55
56
57
58
59
60
61 handle.write(" %i %s\n" % (len(records), length_of_seqs))
62 block=0
63 while True :
64 for record in records :
65 if block==0 :
66
67 """
68 Quoting the PHYLIP version 3.6 documentation:
69
70 The name should be ten characters in length, filled out to
71 the full ten characters by blanks if shorter. Any printable
72 ASCII/ISO character is allowed in the name, except for
73 parentheses ("(" and ")"), square brackets ("[" and "]"),
74 colon (":"), semicolon (";") and comma (","). If you forget
75 to extend the names to ten characters in length by blanks,
76 the program [i.e. PHYLIP] will get out of synchronization
77 with the contents of the data file, and an error message will
78 result.
79
80 Note that Tab characters count as only one character in the
81 species names. Their inclusion can cause trouble.
82 """
83 name = record.id.strip()
84
85
86 for char in "[]()," :
87 name = name.replace(char,"")
88 for char in ":;" :
89 name = name.replace(char,"|")
90
91
92 handle.write(name[:truncate].ljust(truncate))
93 else :
94
95 handle.write(" "*truncate)
96
97 for chunk in range(0,5) :
98 i = block*50 + chunk*10
99 seq_segment = record.seq.tostring()[i:i+10]
100
101
102 handle.write(" %s" % seq_segment)
103 if i+10 > length_of_seqs : break
104 handle.write("\n")
105 block=block+1
106 if block*50 > length_of_seqs : break
107 handle.write("\n")
108
110 """Reads a Phylip alignment file returning an Alignment object iterator.
111
112 Record identifiers are limited to at most 10 characters.
113
114 It only copes with interlaced phylip files! Sequential files won't work
115 where the sequences are split over multiple lines.
116
117 For more information on the file format, please see:
118 http://evolution.genetics.washington.edu/phylip/doc/sequence.html
119 http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
120 """
121
123 line = line.strip()
124 parts = filter(None, line.split())
125 if len(parts)<>2 :
126 return False
127 try :
128 number_of_seqs = int(parts[0])
129 length_of_seqs = int(parts[1])
130 return True
131 except ValueError:
132 return False
133
135 handle = self.handle
136
137 try :
138
139
140 line = self._header
141 del self._header
142 except AttributeError :
143 line = handle.readline()
144
145 if not line: return
146 line = line.strip()
147 parts = filter(None, line.split())
148 if len(parts)<>2 :
149 raise ValueError("First line should have two integers")
150 try :
151 number_of_seqs = int(parts[0])
152 length_of_seqs = int(parts[1])
153 except ValueError:
154 raise ValueError("First line should have two integers")
155
156 assert self._is_header(line)
157
158 if self.records_per_alignment is not None \
159 and self.records_per_alignment <> number_of_seqs :
160 raise ValueError("Found %i records in this alignment, told to expect %i" \
161 % (number_of_seqs, self.records_per_alignment))
162
163 ids = []
164 seqs = []
165
166
167
168 for i in range(0,number_of_seqs) :
169 line = handle.readline().rstrip()
170 ids.append(line[:10].strip())
171 seqs.append([line[10:].strip().replace(" ","")])
172
173
174 line=""
175 while True :
176
177 while ""==line.strip():
178 line = handle.readline()
179 if not line : break
180 if not line : break
181
182 if self._is_header(line) :
183
184 self._header = line
185 break
186
187
188 for i in range(0,number_of_seqs) :
189 seqs[i].append(line.strip().replace(" ",""))
190 line = handle.readline()
191 if (not line) and i+1 < number_of_seqs :
192 raise ValueError("End of file mid-block")
193 if not line : break
194
195 alignment = Alignment(self.alphabet)
196 for i in range(0,number_of_seqs) :
197 seq = "".join(seqs[i])
198 if len(seq)<>length_of_seqs :
199 raise ValueError("Sequence %i length %i, expected length %i" \
200 % (i+1, len(seq), length_of_seqs))
201 alignment.add_sequence(ids[i], seq)
202
203 record = alignment.get_all_seqs()[-1]
204 assert ids[i] == record.id or ids[i] == record.description
205 record.id = ids[i]
206 record.name = ids[i]
207 record.description = ids[i]
208 return alignment
209
210 if __name__=="__main__" :
211 print "Running short mini-test"
212
213 phylip_text=""" 8 286
214 V_Harveyi_ --MKNWIKVA VAAIA--LSA A--------- ---------T VQAATEVKVG
215 B_subtilis MKMKKWTVLV VAALLAVLSA CG-------- ----NGNSSS KEDDNVLHVG
216 B_subtilis MKKALLALFM VVSIAALAAC GAGNDNQSKD NAKDGDLWAS IKKKGVLTVG
217 YA80_HAEIN MKKLLFTTAL LTGAIAFSTF ---------- -SHAGEIADR VEKTKTLLVG
218 FLIY_ECOLI MKLAHLGRQA LMGVMAVALV AG---MSVKS FADEG-LLNK VKERGTLLVG
219 E_coli_Gln --MKSVLKVS LAALTLAFAV S--------- ---------S HAADKKLVVA
220 Deinococcu -MKKSLLSLK LSGLLVPSVL ALS------- -LSACSSPSS TLNQGTLKIA
221 HISJ_E_COL MKKLVLSLSL VLAFSSATAA F--------- ---------- AAIPQNIRIG
222
223 MSGRYFPFTF VKQ--DKLQG FEVDMWDEIG KRNDYKIEYV TANFSGLFGL
224 ATGQSYPFAY KEN--GKLTG FDVEVMEAVA KKIDMKLDWK LLEFSGLMGE
225 TEGTYEPFTY HDKDTDKLTG YDVEVITEVA KRLGLKVDFK ETQWGSMFAG
226 TEGTYAPFTF HDK-SGKLTG FDVEVIRKVA EKLGLKVEFK ETQWDAMYAG
227 LEGTYPPFSF QGD-DGKLTG FEVEFAQQLA KHLGVEASLK PTKWDGMLAS
228 TDTAFVPFEF KQG--DKYVG FDVDLWAAIA KELKLDYELK PMDFSGIIPA
229 MEGTYPPFTS KNE-QGELVG FDVDIAKAVA QKLNLKPEFV LTEWSGILAG
230 TDPTYAPFES KNS-QGELVG FDIDLAKELC KRINTQCTFV ENPLDALIPS
231
232 LETGRIDTIS NQITMTDARK AKYLFADPYV VDG-AQITVR KGNDSIQGVE
233 LQTGKLDTIS NQVAVTDERK ETYNFTKPYA YAG-TQIVVK KDNTDIKSVD
234 LNSKRFDVVA NQVG-KTDRE DKYDFSDKYT TSR-AVVVTK KDNNDIKSEA
235 LNAKRFDVIA NQTNPSPERL KKYSFTTPYN YSG-GVIVTK SSDNSIKSFE
236 LDSKRIDVVI NQVTISDERK KKYDFSTPYT ISGIQALVKK GNEGTIKTAD
237 LQTKNVDLAL AGITITDERK KAIDFSDGYY KSG-LLVMVK ANNNDVKSVK
238 LQANKYDVIV NQVGITPERQ NSIGFSQPYA YSRPEIIVAK NNTFNPQSLA
239 LKAKKIDAIM SSLSITEKRQ QEIAFTDKLY AADSRLVVAK NSDIQP-TVE
240
241 DLAGKTVAVN LGSNFEQLLR DYDKDGKINI KTYDT--GIE HDVALGRADA
242 DLKGKTVAAV LGSNHAKNLE SKDPDKKINI KTYETQEGTL KDVAYGRVDA
243 DVKGKTSAQS LTSNYNKLAT N----AGAKV EGVEGMAQAL QMIQQARVDM
244 DLKGRKSAQS ATSNWGKDAK A----AGAQI LVVDGLAQSL ELIKQGRAEA
245 DLKGKKVGVG LGTNYEEWLR QNV--QGVDV RTYDDDPTKY QDLRVGRIDA
246 DLDGKVVAVK SGTGSVDYAK AN--IKTKDL RQFPNIDNAY MELGTNRADA
247 DLKGKRVGST LGSNYEKQLI DTG---DIKI VTYPGAPEIL ADLVAGRIDA
248 SLKGKRVGVL QGTTQETFGN EHWAPKGIEI VSYQGQDNIY SDLTAGRIDA
249
250 FIMDRLSALE -LIKKT-GLP LQLAGEPFET I-----QNAW PFVDNEKGRK
251 YVNSRTVLIA -QIKKT-GLP LKLAGDPIVY E-----QVAF PFAKDDAHDK
252 TYNDKLAVLN -YLKTSGNKN VKIAFETGEP Q-----STYF TFRKGS--GE
253 TINDKLAVLD -YFKQHPNSG LKIAYDRGDK T-----PTAF AFLQGE--DA
254 ILVDRLAALD -LVKKT-NDT LAVTGEAFSR Q-----ESGV ALRKGN--ED
255 VLHDTPNILY -FIKTAGNGQ FKAVGDSLEA Q-----QYGI AFPKGS--DE
256 AYNDRLVVNY -IINDQ-KLP VRGAGQIGDA A-----PVGI ALKKGN--SA
257 AFQDEVAASE GFLKQPVGKD YKFGGPSVKD EKLFGVGTGM GLRKED--NE
258
259 LQAEVNKALA EMRADGTVEK ISVKWFGADI TK----
260 LRKKVNKALD ELRKDGTLKK LSEKYFNEDI TVEQKH
261 VVDQVNKALK EMKEDGTLSK ISKKWFGEDV SK----
262 LITKFNQVLE ALRQDGTLKQ ISIEWFGYDI TQ----
263 LLKAVNDAIA EMQKDGTLQA LSEKWFGADV TK----
264 LRDKVNGALK TLRENGTYNE IYKKWFGTEP K-----
265 LKDQIDKALT EMRSDGTFEK ISQKWFGQDV GQP---
266 LREALNKAFA EMRADGTYEK LAKKYFDFDV YGG---
267 """
268
269 from cStringIO import StringIO
270 handle = StringIO(phylip_text)
271 count=0
272 for alignment in PhylipIterator(handle) :
273 for record in alignment.get_all_seqs() :
274 count=count+1
275 print record.id
276
277 assert count == 8
278
279 expected="""mkklvlslsl vlafssataa faaipqniri gtdptyapfe sknsqgelvg
280 fdidlakelc krintqctfv enpldalips lkakkidaim sslsitekrq qeiaftdkly
281 aadsrlvvak nsdiqptves lkgkrvgvlq gttqetfgne hwapkgieiv syqgqdniys
282 dltagridaafqdevaaseg flkqpvgkdy kfggpsvkde klfgvgtgmg lrkednelre
283 alnkafaemradgtyeklak kyfdfdvygg""".replace(" ","").replace("\n","").upper()
284 assert record.seq.tostring().replace("-","") == expected
285
286
287
288 phylip_text2="""5 60
289 Tax1 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAG
290 Tax2 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGG
291 Tax3 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGG
292 Tax4 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGG
293 Tax5 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGG
294
295 GAAATGGTCAATATTACAAGGT
296 GAAATGGTCAACATTAAAAGAT
297 GAAATCGTCAATATTAAAAGGT
298 GAAATGGTCAATCTTAAAAGGT
299 GAAATGGTCAATATTAAAAGGT"""
300
301 phylip_text3="""5 60
302 Tax1 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT
303 Tax2 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT
304 Tax3 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT
305 Tax4 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT
306 Tax5 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT"""
307
308 handle = StringIO(phylip_text2)
309 list2 = list(PhylipIterator(handle))
310 handle.close()
311 assert len(list2)==1
312 assert len(list2[0].get_all_seqs())==5
313
314 handle = StringIO(phylip_text3)
315 list3 = list(PhylipIterator(handle))
316 handle.close()
317 assert len(list3)==1
318 assert len(list3[0].get_all_seqs())==5
319
320 for i in range(0,5) :
321 list2[0].get_all_seqs()[i].id == list3[0].get_all_seqs()[i].id
322 list2[0].get_all_seqs()[i].seq.tostring() == list3[0].get_all_seqs()[i].seq.tostring()
323
324
325
326
327 phylip_text4=""" 5 42
328 Turkey AAGCTNGGGC ATTTCAGGGT
329 Salmo gairAAGCCTTGGC AGTGCAGGGT
330 H. SapiensACCGGTTGGC CGTTCAGGGT
331 Chimp AAACCCTTGC CGTTACGCTT
332 Gorilla AAACCCTTGC CGGTACGCTT
333
334 GAGCCCGGGC AATACAGGGT AT
335 GAGCCGTGGC CGGGCACGGT AT
336 ACAGGTTGGC CGTTCAGGGT AA
337 AAACCGAGGC CGGGACACTC AT
338 AAACCATTGC CGGTACGCTT AA"""
339
340
341
342 phylip_text5=""" 5 42
343 Turkey AAGCTNGGGC ATTTCAGGGT
344 GAGCCCGGGC AATACAGGGT AT
345 Salmo gairAAGCCTTGGC AGTGCAGGGT
346 GAGCCGTGGC CGGGCACGGT AT
347 H. SapiensACCGGTTGGC CGTTCAGGGT
348 ACAGGTTGGC CGTTCAGGGT AA
349 Chimp AAACCCTTGC CGTTACGCTT
350 AAACCGAGGC CGGGACACTC AT
351 Gorilla AAACCCTTGC CGGTACGCTT
352 AAACCATTGC CGGTACGCTT AA"""
353
354 phylip_text5a=""" 5 42
355 Turkey AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT
356 Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT
357 H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA
358 Chimp AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT
359 Gorilla AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA"""
360
361 handle = StringIO(phylip_text4)
362 list4 = list(PhylipIterator(handle))
363 handle.close()
364 assert len(list4)==1
365 assert len(list4[0].get_all_seqs())==5
366
367 handle = StringIO(phylip_text5)
368 try :
369 list5 = list(PhylipIterator(handle))
370 assert len(list5)==1
371 assert len(list5[0].get_all_seqs())==5
372 print "That should have failed..."
373 except ValueError :
374 print "Evil multiline non-interlaced example failed as expected"
375 handle.close()
376
377 handle = StringIO(phylip_text5a)
378 list5 = list(PhylipIterator(handle))
379 handle.close()
380 assert len(list5)==1
381 assert len(list4[0].get_all_seqs())==5
382
383 print "Concatenation"
384 handle = StringIO(phylip_text4 + "\n" + phylip_text4)
385 assert len(list(PhylipIterator(handle))) == 2
386
387 handle = StringIO(phylip_text3 + "\n" + phylip_text4 + "\n\n\n" + phylip_text)
388 assert len(list(PhylipIterator(handle))) == 3
389
390 print "OK"
391
392 print "Checking write/read"
393 handle = StringIO()
394 PhylipWriter(handle).write_file(list5)
395 handle.seek(0)
396 list6 = list(PhylipIterator(handle))
397 assert len(list5) == len(list6)
398 for a1,a2 in zip(list5, list6) :
399 assert len(a1.get_all_seqs()) == len(a2.get_all_seqs())
400 for r1, r2 in zip(a1.get_all_seqs(), a2.get_all_seqs()) :
401 assert r1.id == r2.id
402 assert r1.seq.tostring() == r2.seq.tostring()
403 print "Done"
404