Updating to use python3 and updated pysam - Githubissues

hall-lab / bamkit

Tools for common BAM file manipulations

MIT License

2 stars 6 forks source link

Updating to use python3 and updated pysam #5

Open DavidStreid opened 5 months ago

DavidStreid commented 5 months ago

Updating bamkit to use python3 and updated pysam syntax

Changes

python3

print(), exceptions, etc.

pysam

Samfile -> AlignmentFile; AlignedRead -> AlignedSegment [pysam-0.8.1]
AlignedSegment:
- opt() -> get_tag() [pysam-0.8.2]
- is_duplicate
- is_supplementary instead of flagcheck.flag & 2048 == 2048
- cigar -> cigartuples
- qname -> queryname

Testing

vyx-L-HGL63D9FVK:bamkit dstreid$ python3 
Python 3.11.6 (main, Nov  2 2023, 04:39:43) [Clang 14.0.3 (clang-1403.0.22.14.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import bamcleanheader
>>> import bamfilterrg
>>> import bamfixflags
>>> import bamgroupreads
>>> import bamheadrg
>>> import bamlibs
>>> import bamtofastq
>>> exit()