I need to convert a very huge .bam file to .bed file, although I found a solution by using bedops's bam2bed parallel, that parallel support SEG and gnuParallel, the two clusters I can access only support slurm and torque schedulers, and I do not know much about tcsh, I can even not modify the script to meet the require of slurm and torque.
Due to I know a little about Python, I plan to use Python's multiprocessing module to do this, however, the following code raise a weird message:
"Python quit unexpectedly while using the calignmentfile.so plug-in"
# The code here is just a test code, ignore its real meaning.
import multiprocessing as mp
import pysam
def work(read):
return read.query
# return read.split()[0]
if __name__ == '__main__':
cpu = mp.cpu_count()
pool = mp.Pool(cpu)
sam = pysam.AlignmentFile('foo.bam', 'rb')
read = sam.fetch(until_eof=True)
# f = open('foo.text', 'rb')
# results = pool.map(work, f, cpu)
results = pool.map(work, read, cpu)
print(results)
Does this message mean the reads from pysam.AlignmentFile() does not support parallelism, or Python doesn't support this kind of parallel? I use a regular text file test this piece of code, it works well (e.g. the code was commented).
