I am used to
biopython solutions when dealing with sequencing data, but now I wish to switch to more elegant
pysam. So I looked at the manual, but ran into quite bizarre troubles with the first couple of lines using my bam file
import pysam samfile = pysam.AlignmentFile("3_Tms_1_mapped.bam", "rb") for read in samfile.fetch('3_Tms_b3v08_scaf000159'): print(read) samfile.close()
ValueError: fetching by region is not available for SAM files. Well, the file is
bam. I tried to google the error but the only hits I found are the lines in the source code of pysam that check if the file is bam/cram or sam, so somehow
pysam thinks that my bam is a sam. How can I convince it otherwise? I have also noticed that the manual is for python 2.7, that's maybe where the problem comes from...