Fastq Creator ‘bam2fastq’ Method

def bam2fastq(self, bam_filename_list, fastq_filename):
        try:
                with open(fastq_filename, 'w') as fastq_file:

                        for bam_file in bam_filename_list:
                                if os.path.exists(bam_file):
                                        try:
                                                samfile = pysam.Samfile(bam_file, mode="rb",check_header=False,check_sq=False)
                                                for x in samfile.fetch(until_eof=True):
                                                        if x.is_reverse:
                                                                qual = x.qual[::-1]
                                                                seq = reverse_complement(x.seq)
                                                        else:
                                                                qual = x.qual
                                                                seq = x.seq
                                                        fastq_file.write("@%s\n%s\n+\n%s\n" % (x.qname,seq,qual))
                                                samfile.close()
                                        except:
                                                traceback.print_exc()
        except:
                traceback.print_exc()

Like the bam2fastq_picard method, it takes a list of bam filenames and a fastq filename.

It opens the fastq file for writing, calls pysam.Samfile on each bam filename, and writes the results directly to the fastq file.