input file can't be file.vcf.gz?

edgardomortiz / vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

GNU General Public License v3.0

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input file can't be file.vcf.gz? #26

Closed yanzhongsino closed 4 years ago

yanzhongsino commented 4 years ago

helllo, thanks for your software. I met an error while I used the command "vcf2phylip.py -f -o O.chinensis_01,O.octandra_01,O.scaberrima_01,O.scaberrima_02 -i melastoma.filter.vcf.gz" Then I got the message. Traceback (most recent call last): File "/DATA4/Liang/yanzhong/software/vcf2phylip-master/vcf2phylip.py", line 430, in main() File "/DATA4/Liang/yanzhong/software/vcf2phylip-master/vcf2phylip.py", line 124, in main if line.startswith("#CHROM"): TypeError: startswith first arg must be bytes or a tuple of bytes, not str

any reply will be welcomed.

edgardomortiz commented 4 years ago

The input can be compressed, no problem. The error I can see right now is the otugroup definition, just a single sample is allowed to be defined as outgroup. Changing that solves the problem?

If not, perhaps something with your python's version (I wrote it for > 3.7)? Also, do you have the latest commit? if you are not sure simply erase your copy of vcf2phylip and re-clone with:

git clone https://github.com/edgardomortiz/vcf2phylip/

Edgardo

edgardomortiz commented 4 years ago

I will close the issue now, please feel free to re-open it

danrlu commented 4 years ago

For anyone else searching for this error: Python 3.7.3 with vcf2phylip 2.0 gave this error. Python 2.7.13 with vcf2phylip 2.0 works. Python 3.7.3 with vcf2phylip 2.3 works.

Thank you for such a useful tool!