sridnona / cb_sniffer

mutation(barcode) caller for 10x single cell data

GNU General Public License v3.0

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pysam version #1

Closed TimoTrefzer closed 5 years ago

TimoTrefzer commented 5 years ago

Hello,

I was wondering which version of pysam you are using. Because I get the following error and think it might be due to changes in pysams variables:

File "scripts/cb_sniffer.py", line 347, in barcode_counts = x.count_barcodes(bam_file, bars, x.classify(), mq, bq) File "scripts/cb_sniffer.py", line 77, in count_barcodes with pysam.AlignmentFile(bam_fil, 'rb') as pile: AttributeError: 'module' object has no attribute 'AlignmentFile'

Cheers

TimoTrefzer commented 5 years ago

For me it worked now with version 0.15.3 from bioconda

sridnona commented 5 years ago

hi @TimoTrefzer

If you look at the code line6-7

print(pysam.version)

0.14.1

the docker container attached has the same pysam version, please let me know if you still have issues.

Thanks Sid

sridnona commented 5 years ago

Hi @TimoTrefzer closing this happy to reopen it if you still see issues.

Thanks Sid