INNER CODE UNIT · Python

_generate_index

Gabaldonlab/redundans · bin/FastaIndex.py:107

    def _generate_index(self): 
        """Return fasta records"""
        if self.verbose:
            self.log("Generating FastA index...\n")
        header, seq = "", []
        offset = pi = 0
        self.id2stats = {}
        with open(self.faidx, 'w') as out:
            for i, l in enumerate(iter(self.handle.readline, ''), 1): 
                if l.startswith(">"):
                    self.__process_seqentry(out, header, seq, offset, pi)
                    # mark that there is whitespace in headers
                    if len(l[:-1].split())>1:
                        self.whitespaces_in_headers = True
                    header = l
                    offset = self.handle.tell() 
                    seq = []
                    pi = i

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