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10 """Bio.SeqIO support for the "fasta" (aka FastA or Pearson) file format.
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12 You are expected to use this module via the Bio.SeqIO functions."""
13
14 from Bio.Alphabet import single_letter_alphabet
15 from Bio.Seq import Seq
16 from Bio.SeqRecord import SeqRecord
17 from Interfaces import SequentialSequenceWriter
18
19
21 """Generator function to iterate over Fasta records (as SeqRecord objects).
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23 handle - input file
24 alphabet - optional alphabet
25 title2ids - A function that, when given the title of the FASTA
26 file (without the beginning >), will return the id, name and
27 description (in that order) for the record as a tuple of strings.
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29 If this is not given, then the entire title line will be used
30 as the description, and the first word as the id and name.
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32 Note that use of title2ids matches that of Bio.Fasta.SequenceParser
33 but the defaults are slightly different.
34 """
35
36 while True :
37 line = handle.readline()
38 if line == "" : return
39 if line[0] == ">" :
40 break
41
42 while True :
43 if line[0]!=">" :
44 raise ValueError("Records in Fasta files should start with '>' character")
45 if title2ids :
46 id, name, descr = title2ids(line[1:].rstrip())
47 else :
48 descr = line[1:].rstrip()
49 id = descr.split()[0]
50 name = id
51
52 lines = []
53 line = handle.readline()
54 while True:
55 if not line : break
56 if line[0] == ">": break
57
58
59
60 lines.append(line.rstrip().replace(" ","").replace("\r",""))
61 line = handle.readline()
62
63
64 yield SeqRecord(Seq("".join(lines), alphabet),
65 id = id, name = name, description = descr)
66
67 if not line : return
68 assert False, "Should not reach this line"
69
71 """Class to write Fasta format files."""
72 - def __init__(self, handle, wrap=60, record2title=None):
73 """Create a Fasta writer.
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75 handle - Handle to an output file, e.g. as returned
76 by open(filename, "w")
77 wrap - Optional line length used to wrap sequence lines.
78 Defaults to wrapping the sequence at 60 characters
79 Use zero (or None) for no wrapping, giving a single
80 long line for the sequence.
81 record2title - Optional function to return the text to be
82 used for the title line of each record. By default the
83 a combination of the record.id and record.description
84 is used. If the record.description starts with the
85 record.id, then just the record.description is used.
86
87 You can either use:
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89 myWriter = FastaWriter(open(filename,"w"))
90 writer.write_file(myRecords)
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92 Or, follow the sequential file writer system, for example:
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94 myWriter = FastaWriter(open(filename,"w"))
95 writer.write_header() # does nothing for Fasta files
96 ...
97 Multiple calls to writer.write_record() and/or writer.write_records()
98 ...
99 writer.write_footer() # does nothing for Fasta files
100 writer.close()
101 """
102 SequentialSequenceWriter.__init__(self, handle)
103
104 self.wrap = None
105 if wrap :
106 if wrap < 1 :
107 raise ValueError
108 self.wrap = wrap
109 self.record2title = record2title
110
144
145 if __name__ == "__main__" :
146 print "Running quick self test"
147
148 import os
149 from Bio.Alphabet import generic_protein, generic_nucleotide
150
151
152
153 fna_filename = "NC_005213.fna"
154 faa_filename = "NC_005213.faa"
155
161
174
175 if os.path.isfile(fna_filename) :
176 print "--------"
177 print "FastaIterator (single sequence)"
178 iterator = FastaIterator(open(fna_filename, "r"), alphabet=generic_nucleotide, title2ids=genbank_name_function)
179 count=0
180 for record in iterator :
181 count=count+1
182 print_record(record)
183 assert count == 1
184 print str(record.__class__)
185
186 if os.path.isfile(faa_filename) :
187 print "--------"
188 print "FastaIterator (multiple sequences)"
189 iterator = FastaIterator(open(faa_filename, "r"), alphabet=generic_protein, title2ids=genbank_name_function)
190 count=0
191 for record in iterator :
192 count=count+1
193 print_record(record)
194 break
195 assert count>0
196 print str(record.__class__)
197
198 from cStringIO import StringIO
199 print "--------"
200 print "FastaIterator (empty input file)"
201
202 iterator = FastaIterator(StringIO(""))
203 count = 0
204 for record in iterator :
205 count = count+1
206 assert count==0
207
208 print "Done"
209