51 lines
1.3 KiB
Python
51 lines
1.3 KiB
Python
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#!/usr/bin/env python
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import string
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class fasta_record:
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"Record containing one FASTA sequence"
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def __init__(self, id, seq):
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self.id = id
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self.seq = seq
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def __str__(self):
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return '['+self.id+" "+self.seq+']'
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class fasta_file:
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"Iterable object based on FASTA file format"
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def __init__(self, filename, cleanup=True):
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"cleanup removes spaces from fasta text (default: True)"
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self.filename = filename
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self.fin = open(self.filename)
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self._cleanup = cleanup
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def RecordGenerator(self):
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line = self.fin.readline().rstrip()
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assert line[0] == ">"
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id = line[1:]
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seq = ""
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for line in self.fin:
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line = line.rstrip()
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if line[0] == ">":
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yield fasta_record(id, seq)
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id = line[1:]
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seq = ""
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else:
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if self._cleanup:
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seq += line.replace(" ","")
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else:
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seq += line
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yield fasta_record(id, seq) # Yield last seq
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raise StopIteration # No more lines
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def __iter__(self):
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return self.RecordGenerator()
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if __name__ == "__main__":
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print "Testing fast.py on file 5seqs.fa..."
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for fasta_rec in fasta_file("5seqs.fa"):
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print fasta_rec
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