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Python Package Import Incompatibility: pysam #374
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Secondary Issue related to HPC Snakemake Upgrade #371Dry-running the second half of the ChIP-seq pipeline causes a python
The import error is due to the version of python that is bundled with snakemake (see: |
UpdateAfter closer inspection, it looks that pysam is not actively being used. The function call to def normalize_bam_file_chromosomes(bamfns, obamfns=[], suffix='.common_chrom.bam'):
from pysam import Samfile, FastaFile
counts = []
for bamfn1 in bamfns :
bam1 = Samfile(bamfn1)
cnt1 = Counter()
for aread1 in bam1 :
if aread1.is_unmapped :
continue
cnt1[aread1.reference_name] += 1
bam1.close()
counts.append(cnt1)
common = None
for cnt in counts :
if common != None :
common = common.intersection(cnt)
else :
common = set(cnt) Changes will be made in the following locations:
Permanent solution:Remove the snakemake |
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