I am writing a function of a class to convert a sam file to bam file, then sort it and index it in python (I know it is easy to fulfill in bash, but it does not hurt to learn more).
A sam file has already been generated in the defined directory (cwd) by another function of the class already.
Here is the code:
def sam2bam(self):
"""
return a sorted and index bam file in the working directory
"""
if str(self.fq)[7:9] == '24':
# create bam
comnd = "samtools view -bS " + str(self.fq)[0:10] + ".sam > " + str(self.fq)[0:10] + ".bam"
print("Converting sam to bam ... (executed command: {})\n".format(comnd))
comnd_input = shlex.split(comnd)
with open((str(self.fq)[0:10] + '.bam'), 'w') as f:
Popen(comnd_input, stdout = f, stderr = PIPE, cwd = 'G24/' + str(self.fq))
# sort bam
comnd2 = "samtools sort " + str(self.fq)[0:10] + ".bam -o " + str(self.fq)[0:10] + ".sorted.bam"
print('Sorting bam ... (executed command: {}\n)'.format(comnd2))
comnd_input2 = shlex.split(comnd2)
with open((str(self.fq)[0:10] + 'sorted.bam'), 'w') as f_sort:
Popen(comnd_input2, stdout = f_sort, stderr = PIPE, cwd = 'G24/' + str(self.fq))
# index bam
comnd3 = "samtools index " + str(self.fq)[0:10] + ".sorted.bam"
print('Indexing bam ... (executed command: {}\n)'.format(comnd3))
comnd_input3 = shlex.split(comnd3)
with open((str(self.fq)[0:10] + 'sorted.bam'), 'w') as f_index:
Popen(comnd_input3, stdout = f_index, stderr = PIPE, cwd = 'G24/' + str(self.fq))
But nothing came out
I tried:
Popen(comnd_input, stdout = PIPE, stderr = PIPE, cwd = 'G24/' + str(self.fq))
yet nothing either. Tried save it as a variable and do .communicate(), nothing.
So I don't know what wrong I did?
thanks,
Xp
