Hi there! I have run into a minor annoying thing which is that it seems like mutyper targets can't accept gzipped/bgzipped bed files in the --bed section. I get the following error:
Traceback (most recent call last):
File "/net/harris/vol1/home/beichman/.local/bin/mutyper", line 8, in
sys.exit(main())
File "/net/harris/vol1/home/beichman/.local/lib/python3.7/site-packages/mutyper/cli.py", line 336, in main
args.func(args)
File "/net/harris/vol1/home/beichman/.local/lib/python3.7/site-packages/mutyper/cli.py", line 152, in targets
sizes = ancestor.targets(args.bed)
File "/net/harris/vol1/home/beichman/.local/lib/python3.7/site-packages/mutyper/ancestor.py", line 167, in targets
for line in bed:
File "/net/gs/vol3/software/modules-sw/python/3.7.7/Linux/CentOS7/x86_64/lib/python3.7/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
It's not a huge deal (can just unzip the bed) but since some of the beds I'm working with are very large it would be a nice feature to be able to accept a bed.gz file the way bcftools does, if possible! :) (I've confirmed that bcftools view -R *.bed.gz works so it doesn't seem to be a bed file formatting issue)
Hi there! I have run into a minor annoying thing which is that it seems like mutyper targets can't accept gzipped/bgzipped bed files in the --bed section. I get the following error:
Traceback (most recent call last): File "/net/harris/vol1/home/beichman/.local/bin/mutyper", line 8, in
sys.exit(main())
File "/net/harris/vol1/home/beichman/.local/lib/python3.7/site-packages/mutyper/cli.py", line 336, in main
args.func(args)
File "/net/harris/vol1/home/beichman/.local/lib/python3.7/site-packages/mutyper/cli.py", line 152, in targets
sizes = ancestor.targets(args.bed)
File "/net/harris/vol1/home/beichman/.local/lib/python3.7/site-packages/mutyper/ancestor.py", line 167, in targets
for line in bed:
File "/net/gs/vol3/software/modules-sw/python/3.7.7/Linux/CentOS7/x86_64/lib/python3.7/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
It's not a huge deal (can just unzip the bed) but since some of the beds I'm working with are very large it would be a nice feature to be able to accept a bed.gz file the way bcftools does, if possible! :) (I've confirmed that bcftools view -R *.bed.gz works so it doesn't seem to be a bed file formatting issue)