f1 = pysam.VariantFile("test.vcf.gz")
for f in f1.fetch(str(chr), int(start), int(end)):
if f:
print "yes"
else :
print "hello"
In the above example Its not printing "hello" even for cases which doesn't have entry into VCF. I want to print program "hello" for cases where VariantFile doesn't have variants records.
Its their a way to do this ?
Thanks
•
written
by
always_learning
SInce I have a small files need to extracted from VCF file so i jus used hash and then search in hash so finally I was able to accomplished this task but stiil i have no idea why its not printing "hello" even for cases which doesn't have entry into VCF
Pysam returns an iterator for the fetch call, so that condition will be always be true. You can query for an attribute of the VariantRecord (e.g. contig, pos etc.) to check if it's empty.
for f in f1.fetch(str(chr), int(start), int(end)):
# This will return an empty list if a variant is not present at that location.
if [r.contig for r in f]:
print True
else:
print False
I'd like to suggest to write python3-compatible code, especially when you are sharing examples. In this case you have to adapt the print statements to print(True) and print(False). As such, users who stumble upon your solution won't have issues running your code.
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Try:
instead of the
forloop.Thanks Ryan, Its not working. I tried this earlier as well.
What do you get if you print
ffor positions which are not in the vcf?Its not going inside else condition.
There shouldn't be an
elsecondition, since there shouldn't be aforloop in this case in question.And looking at how
flooks like doesn't depend on if else statement, you just need to now what fetch returns for a position you think isn't included in the vcf.Even this is not working as well.
What do you get if you print
f1.fetch(str(chr), int(start), int(end))for positions which are not in the vcf?Reagrdless of absence or present its proting iterator object. I checked for object condition as well but no luck.
The TabixIterator is always
True, regardless of precense or absence of that variant.yes and Thats why its never going to else condition.
Exactly. What are you trying to achieve? This issue probably has a better solution.
you means other ways Using Pysam ?