Hi, This question is for those who are familiar with pysam.
pysam is used as follows:
samfile = pysam.AlignmentFile('file.bam', 'rb')
In the examples shown in the documentation, he always ends the code with:
samfile.close()
Similar to when closing a file in python.
I can't find anything about the exact purpose of this in the documentation for pysam. Is it similar to when closing a regular file?
I'm asking because I wan't to create a function where samfile is returned to the caller function. Would I then need to close the samfile in the caller function?
eg.:
def open_bam(file):
samfile = pysam.AlignmentFile(file, 'rb')
return samfile
samfile.close()
And then use it as follows:
def analyze_bam(sfile):
for read in sfile.fetch():
print read
sfile.close()
Or can I simply skip closing it in analyze_bam()?
If you open a file in a function and want to return it, then you can't close it. In your open_bam() example, remove the last line, which will never be reached.
Anyway, yes, closing samfile is the same as closing a regular file. In theory python will do it for you when the process finishes, but I've seen cases where this doesn't happen (mostly with images in matplotlib).
Okay, so if I remove samfile.close() from open_bam() and keep return samfile, could I then do something like this?:
bam_graph(open_bam('filename.bam'))
def bam_graph(samfile):
Code to produce graph and then end it with:
samfile.close()
Will it be okay then to structure my script like this or is it possible that this will invoke problems further down the road?
That'd be fine.
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