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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 import string
24
25 from Bio.Align import Generic
26
28 """Saves information from a blast header.
29
30 Members:
31 application The name of the BLAST flavor that generated this data.
32 version Version of blast used.
33 date Date this data was generated.
34 reference Reference for blast.
35
36 query Name of query sequence.
37 query_letters Number of letters in the query sequence. (int)
38
39 database Name of the database.
40 database_sequences Number of sequences in the database. (int)
41 database_letters Number of letters in the database. (int)
42
43 """
56
58 """Stores information about one hit in the descriptions section.
59
60 Members:
61 title Title of the hit.
62 score Number of bits. (int)
63 bits Bit score. (float)
64 e E value. (float)
65 num_alignments Number of alignments for the same subject. (int)
66
67 """
69 self.title = ''
70 self.score = None
71 self.bits = None
72 self.e = None
73 self.num_alignments = None
75 return "%-66s %5s %s" % (self.title, self.score, self.e)
76
78 """Stores information about one hit in the alignments section.
79
80 Members:
81 title Name.
82 hit_id Hit identifier. (str)
83 hit_def Hit definition. (str)
84 length Length. (int)
85 hsps A list of HSP objects.
86
87 """
89 self.title = ''
90 self.hit_id = ''
91 self.hit_def = ''
92 self.length = None
93 self.hsps = []
95 lines = []
96 titles = string.split(self.title, '\n')
97 for i in range(len(titles)):
98 if i:
99 lines.append(" ")
100 lines.append("%s\n" % titles[i])
101 lines.append(" Length = %s\n" % self.length)
102 return string.join(lines, '')
103
105 """Stores information about one hsp in an alignment hit.
106
107 Members:
108 score BLAST score of hit. (float)
109 bits Number of bits for that score. (float)
110 expect Expect value. (float)
111 num_alignments Number of alignments for same subject. (int)
112 identities Number of identities/total aligned. tuple of (int, int)
113 positives Number of positives/total aligned. tuple of (int, int)
114 gaps Numer of gaps/total aligned. tuple of (int, int)
115 align_length Length of the alignment. (int)
116 strand Tuple of (query, target) strand.
117 frame Tuple of 1 or 2 frame shifts, depending on the flavor.
118
119 query The query sequence.
120 query_start The start residue for the query sequence. (1-based)
121 query_end The end residue for the query sequence. (1-based)
122 match The match sequence.
123 sbjct The sbjct sequence.
124 sbjct_start The start residue for the sbjct sequence. (1-based)
125 sbjct_end The end residue for the sbjct sequence. (1-based)
126
127 Not all flavors of BLAST return values for every attribute:
128 score expect identities positives strand frame
129 BLASTP X X X X
130 BLASTN X X X X X
131 BLASTX X X X X X
132 TBLASTN X X X X X
133 TBLASTX X X X X X/X
134
135 Note: for BLASTX, the query sequence is shown as a protein sequence,
136 but the numbering is based on the nucleotides. Thus, the numbering
137 is 3x larger than the number of amino acid residues. A similar effect
138 can be seen for the sbjct sequence in TBLASTN, and for both sequences
139 in TBLASTX.
140
141 Also, for negative frames, the sequence numbering starts from
142 query_start and counts down.
143
144 """
146 self.score = None
147 self.bits = None
148 self.expect = None
149 self.num_alignments = None
150 self.identities = (None, None)
151 self.positives = (None, None)
152 self.gaps = (None, None)
153 self.align_length = None
154 self.strand = (None, None)
155 self.frame = ()
156
157 self.query = ''
158 self.query_start = None
159 self.query_end = None
160 self.match = ''
161 self.sbjct = ''
162 self.sbjct_start = None
163 self.sbjct_end = None
164
166 """Holds information about a multiple alignment.
167
168 Members:
169 alignment A list of tuples (name, start residue, sequence, end residue).
170
171 The start residue is 1-based. It may be blank, if that sequence is
172 not aligned in the multiple alignment.
173
174 """
177
179 """Retrieve generic alignment object for the given alignment.
180
181 Instead of the tuples, this returns an Alignment object from
182 Bio.Align.Generic, through which you can manipulate and query
183 the object.
184
185 alphabet is the specified alphabet for the sequences in the code (for
186 example IUPAC.IUPACProtein.
187
188 Thanks to James Casbon for the code.
189 """
190 seq_parts = []
191 seq_names = []
192 parse_number = 0
193 n = 0
194 for name, start, seq, end in self.alignment:
195 if name == 'QUERY':
196 parse_number = parse_number + 1
197 n = 0
198
199 if parse_number == 1:
200 seq_parts.append(seq)
201 seq_names.append(name)
202 else:
203 seq_parts[n] = seq_parts[n] + seq
204 n = n + 1
205
206 generic = Generic.Alignment(alphabet)
207 for (name,seq) in zip(seq_names,seq_parts):
208 generic.add_sequence(name, seq)
209
210 return generic
211
213 """Holds information from a PSI-BLAST round.
214
215 Members:
216 number Round number. (int)
217 reused_seqs Sequences in model, found again. List of Description objects.
218 new_seqs Sequences not found, or below threshold. List of Description.
219 alignments A list of Alignment objects.
220 multiple_alignment A MultipleAlignment object.
221
222 """
224 self.number = None
225 self.reused_seqs = []
226 self.new_seqs = []
227 self.alignments = []
228 self.multiple_alignment = None
229
231 """Holds information about a database report.
232
233 Members:
234 database_name List of database names. (can have multiple dbs)
235 num_letters_in_database Number of letters in the database. (int)
236 num_sequences_in_database List of number of sequences in the database.
237 posted_date List of the dates the databases were posted.
238 ka_params A tuple of (lambda, k, h) values. (floats)
239 gapped # XXX this isn't set right!
240 ka_params_gap A tuple of (lambda, k, h) values. (floats)
241
242 """
251
253 """Holds information about the parameters.
254
255 Members:
256 matrix Name of the matrix.
257 gap_penalties Tuple of (open, extend) penalties. (floats)
258 sc_match Match score for nucleotide-nucleotide comparison
259 sc_mismatch Mismatch penalty for nucleotide-nucleotide comparison
260 num_hits Number of hits to the database. (int)
261 num_sequences Number of sequences. (int)
262 num_good_extends Number of extensions. (int)
263 num_seqs_better_e Number of sequences better than e-value. (int)
264 hsps_no_gap Number of HSP's better, without gapping. (int)
265 hsps_prelim_gapped Number of HSP's gapped in prelim test. (int)
266 hsps_prelim_gapped_attemped Number of HSP's attempted in prelim. (int)
267 hsps_gapped Total number of HSP's gapped. (int)
268 query_length Length of the query. (int)
269 query_id Identifier of the query sequence. (str)
270 database_length Number of letters in the database. (int)
271 effective_hsp_length Effective HSP length. (int)
272 effective_query_length Effective length of query. (int)
273 effective_database_length Effective length of database. (int)
274 effective_search_space Effective search space. (int)
275 effective_search_space_used Effective search space used. (int)
276 frameshift Frameshift window. Tuple of (int, float)
277 threshold Threshold. (int)
278 window_size Window size. (int)
279 dropoff_1st_pass Tuple of (score, bits). (int, float)
280 gap_x_dropoff Tuple of (score, bits). (int, float)
281 gap_x_dropoff_final Tuple of (score, bits). (int, float)
282 gap_trigger Tuple of (score, bits). (int, float)
283 blast_cutoff Tuple of (score, bits). (int, float)
284 """
314
315 -class Blast(Header, DatabaseReport, Parameters):
316 """Saves the results from a blast search.
317
318 Members:
319 descriptions A list of Description objects.
320 alignments A list of Alignment objects.
321 multiple_alignment A MultipleAlignment object.
322 + members inherited from base classes
323
324 """
332
333 -class PSIBlast(Header, DatabaseReport, Parameters):
334 """Saves the results from a blastpgp search.
335
336 Members:
337 rounds A list of Round objects.
338 converged Whether the search converged.
339 + members inherited from base classes
340
341 """
348