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6 """Record classes to hold BLAST output.
7
8 Classes:
9 Blast Holds all the information from a blast search.
10 PSIBlast Holds all the information from a psi-blast search.
11
12 Header Holds information from the header.
13 Description Holds information about one hit description.
14 Alignment Holds information about one alignment hit.
15 HSP Holds information about one HSP.
16 MultipleAlignment Holds information about a multiple alignment.
17 DatabaseReport Holds information from the database report.
18 Parameters Holds information from the parameters.
19
20 """
21
22
23 from Bio.Align import Generic
24
26 """Saves information from a blast header.
27
28 Members:
29 application The name of the BLAST flavor that generated this data.
30 version Version of blast used.
31 date Date this data was generated.
32 reference Reference for blast.
33
34 query Name of query sequence.
35 query_letters Number of letters in the query sequence. (int)
36
37 database Name of the database.
38 database_sequences Number of sequences in the database. (int)
39 database_letters Number of letters in the database. (int)
40
41 """
43 self.application = ''
44 self.version = ''
45 self.date = ''
46 self.reference = ''
47
48 self.query = ''
49 self.query_letters = None
50
51 self.database = ''
52 self.database_sequences = None
53 self.database_letters = None
54
56 """Stores information about one hit in the descriptions section.
57
58 Members:
59 title Title of the hit.
60 score Number of bits. (int)
61 bits Bit score. (float)
62 e E value. (float)
63 num_alignments Number of alignments for the same subject. (int)
64
65 """
67 self.title = ''
68 self.score = None
69 self.bits = None
70 self.e = None
71 self.num_alignments = None
73 return "%-66s %5s %s" % (self.title, self.score, self.e)
74
76 """Stores information about one hit in the alignments section.
77
78 Members:
79 title Name.
80 hit_id Hit identifier. (str)
81 hit_def Hit definition. (str)
82 length Length. (int)
83 hsps A list of HSP objects.
84
85 """
87 self.title = ''
88 self.hit_id = ''
89 self.hit_def = ''
90 self.length = None
91 self.hsps = []
96
98 """Stores information about one hsp in an alignment hit.
99
100 Members:
101 score BLAST score of hit. (float)
102 bits Number of bits for that score. (float)
103 expect Expect value. (float)
104 num_alignments Number of alignments for same subject. (int)
105 identities Number of identities (int) if using the XML parser.
106 Tuple of numer of identities/total aligned (int, int)
107 if using the (obsolete) plain text parser.
108 positives Number of positives (int) if using the XML parser.
109 Tuple of numer of positives/total aligned (int, int)
110 if using the (obsolete) plain text parser.
111 gaps Number of gaps (int) if using the XML parser.
112 Tuple of numer of gaps/total aligned (int, int) if
113 using the (obsolete) plain text parser.
114 align_length Length of the alignment. (int)
115 strand Tuple of (query, target) strand.
116 frame Tuple of 1 or 2 frame shifts, depending on the flavor.
117
118 query The query sequence.
119 query_start The start residue for the query sequence. (1-based)
120 query_end The end residue for the query sequence. (1-based)
121 match The match sequence.
122 sbjct The sbjct sequence.
123 sbjct_start The start residue for the sbjct sequence. (1-based)
124 sbjct_end The end residue for the sbjct sequence. (1-based)
125
126 Not all flavors of BLAST return values for every attribute:
127 score expect identities positives strand frame
128 BLASTP X X X X
129 BLASTN X X X X X
130 BLASTX X X X X X
131 TBLASTN X X X X X
132 TBLASTX X X X X X/X
133
134 Note: for BLASTX, the query sequence is shown as a protein sequence,
135 but the numbering is based on the nucleotides. Thus, the numbering
136 is 3x larger than the number of amino acid residues. A similar effect
137 can be seen for the sbjct sequence in TBLASTN, and for both sequences
138 in TBLASTX.
139
140 Also, for negative frames, the sequence numbering starts from
141 query_start and counts down.
142
143 """
145 self.score = None
146 self.bits = None
147 self.expect = None
148 self.num_alignments = None
149 self.identities = (None, None)
150 self.positives = (None, None)
151 self.gaps = (None, None)
152 self.align_length = None
153 self.strand = (None, None)
154 self.frame = ()
155
156 self.query = ''
157 self.query_start = None
158 self.query_end = None
159 self.match = ''
160 self.sbjct = ''
161 self.sbjct_start = None
162 self.sbjct_end = None
163
165 lines = ["Score %i (%i bits), expectation %0.1e, alignment length %i" \
166 % (self.score, self.bits, self.expect, self.align_length)]
167 if self.align_length < 50 :
168 lines.append("Query:%s %s %s" % (str(self.query_start).rjust(8),
169 str(self.query),
170 str(self.query_end)))
171 lines.append(" %s" \
172 % (str(self.match)))
173 lines.append("Sbjct:%s %s %s" % (str(self.sbjct_start).rjust(8),
174 str(self.sbjct),
175 str(self.sbjct_end)))
176 else :
177 lines.append("Query:%s %s...%s %s" \
178 % (str(self.query_start).rjust(8),
179 str(self.query)[:45],
180 str(self.query)[-3:],
181 str(self.query_end)))
182 lines.append(" %s...%s" \
183 % (str(self.match)[:45],
184 str(self.match)[-3:]))
185 lines.append("Sbjct:%s %s...%s %s" \
186 % (str(self.sbjct_start).rjust(8),
187 str(self.sbjct)[:45],
188 str(self.sbjct)[-3:],
189 str(self.sbjct_end)))
190 return "\n".join(lines)
191
193 """Holds information about a multiple alignment.
194
195 Members:
196 alignment A list of tuples (name, start residue, sequence, end residue).
197
198 The start residue is 1-based. It may be blank, if that sequence is
199 not aligned in the multiple alignment.
200
201 """
204
206 """Retrieve generic alignment object for the given alignment.
207
208 Instead of the tuples, this returns an Alignment object from
209 Bio.Align.Generic, through which you can manipulate and query
210 the object.
211
212 alphabet is the specified alphabet for the sequences in the code (for
213 example IUPAC.IUPACProtein.
214
215 Thanks to James Casbon for the code.
216 """
217 seq_parts = []
218 seq_names = []
219 parse_number = 0
220 n = 0
221 for name, start, seq, end in self.alignment:
222 if name == 'QUERY':
223 parse_number = parse_number + 1
224 n = 0
225
226 if parse_number == 1:
227 seq_parts.append(seq)
228 seq_names.append(name)
229 else:
230 seq_parts[n] = seq_parts[n] + seq
231 n = n + 1
232
233 generic = Generic.Alignment(alphabet)
234 for (name,seq) in zip(seq_names,seq_parts):
235 generic.add_sequence(name, seq)
236
237 return generic
238
240 """Holds information from a PSI-BLAST round.
241
242 Members:
243 number Round number. (int)
244 reused_seqs Sequences in model, found again. List of Description objects.
245 new_seqs Sequences not found, or below threshold. List of Description.
246 alignments A list of Alignment objects.
247 multiple_alignment A MultipleAlignment object.
248
249 """
251 self.number = None
252 self.reused_seqs = []
253 self.new_seqs = []
254 self.alignments = []
255 self.multiple_alignment = None
256
258 """Holds information about a database report.
259
260 Members:
261 database_name List of database names. (can have multiple dbs)
262 num_letters_in_database Number of letters in the database. (int)
263 num_sequences_in_database List of number of sequences in the database.
264 posted_date List of the dates the databases were posted.
265 ka_params A tuple of (lambda, k, h) values. (floats)
266 gapped # XXX this isn't set right!
267 ka_params_gap A tuple of (lambda, k, h) values. (floats)
268
269 """
278
280 """Holds information about the parameters.
281
282 Members:
283 matrix Name of the matrix.
284 gap_penalties Tuple of (open, extend) penalties. (floats)
285 sc_match Match score for nucleotide-nucleotide comparison
286 sc_mismatch Mismatch penalty for nucleotide-nucleotide comparison
287 num_hits Number of hits to the database. (int)
288 num_sequences Number of sequences. (int)
289 num_good_extends Number of extensions. (int)
290 num_seqs_better_e Number of sequences better than e-value. (int)
291 hsps_no_gap Number of HSP's better, without gapping. (int)
292 hsps_prelim_gapped Number of HSP's gapped in prelim test. (int)
293 hsps_prelim_gapped_attemped Number of HSP's attempted in prelim. (int)
294 hsps_gapped Total number of HSP's gapped. (int)
295 query_length Length of the query. (int)
296 query_id Identifier of the query sequence. (str)
297 database_length Number of letters in the database. (int)
298 effective_hsp_length Effective HSP length. (int)
299 effective_query_length Effective length of query. (int)
300 effective_database_length Effective length of database. (int)
301 effective_search_space Effective search space. (int)
302 effective_search_space_used Effective search space used. (int)
303 frameshift Frameshift window. Tuple of (int, float)
304 threshold Threshold. (int)
305 window_size Window size. (int)
306 dropoff_1st_pass Tuple of (score, bits). (int, float)
307 gap_x_dropoff Tuple of (score, bits). (int, float)
308 gap_x_dropoff_final Tuple of (score, bits). (int, float)
309 gap_trigger Tuple of (score, bits). (int, float)
310 blast_cutoff Tuple of (score, bits). (int, float)
311 """
341
342 -class Blast(Header, DatabaseReport, Parameters):
343 """Saves the results from a blast search.
344
345 Members:
346 descriptions A list of Description objects.
347 alignments A list of Alignment objects.
348 multiple_alignment A MultipleAlignment object.
349 + members inherited from base classes
350
351 """
359
360 -class PSIBlast(Header, DatabaseReport, Parameters):
361 """Saves the results from a blastpgp search.
362
363 Members:
364 rounds A list of Round objects.
365 converged Whether the search converged.
366 + members inherited from base classes
367
368 """
375