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1 #!/usr/bin/env python
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2
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3
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4 """Read GenBank flat files.
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5
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6 Currently only reads sequence data and not annotations.
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7
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8 """
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9 from corebio.utils import *
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10 from corebio.seq import *
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11
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12
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13 names = ( 'genbank',)
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14 extensions = ('gb','genbank', 'gbk')
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15
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16
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17
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18 def read(fin, alphabet=None):
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19 """Read and parse a file of genbank records.
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20
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21 Args:
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22 fin -- A stream or file to read
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23 alphabet -- The expected alphabet of the data, if given
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24
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25 Returns:
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26 SeqList -- A list of sequences
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27
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28 Raises:
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29 ValueError -- If the file is unparsable
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30 """
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31 seqs = [ s for s in iterseq(fin, alphabet)]
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32 return SeqList(seqs)
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33
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34
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35 def iterseq(fin, alphabet=None):
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36 """ Iterate over genbank records
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37
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38 Args:
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39 fin -- A stream or file to read
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40 alphabet -- The expected alphabet of the data, if given
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41
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42 Yeilds:
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43 Seq -- One alphabetic sequence at a time.
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44
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45 Raises:
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46 ValueError -- If the file is unparsable
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47 """
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48 alphabet = Alphabet(alphabet)
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49
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50 seq = []
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51
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52 def notblank(string) :
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53 return not isblank(string)
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54
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55 lines = Reiterate(iter(fin))
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56
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57
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58 while True :
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59 line = lines.filter( notblank )
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60 if not line.startswith('LOCUS') :
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61 raise ValueError(
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62 "Cannot find start of record at line %d"% lines.index() )
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63
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64 line = lines.filter(lambda s : s.startswith('ORIGIN')
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65 or s.startswith('//') )
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66
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67 if line.startswith('//') :
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68 # No sequence data
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69 yield Seq( '', alphabet)
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70 else:
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71 for line in lines :
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72 if line.startswith('//') :
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73 yield Seq( ''.join(seq), alphabet)
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74 seq = []
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75 break
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76 seq.extend( line.split()[1:] )
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77
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78
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79
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80
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85 |
