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error about Line 123 and 419 in vcf2phylip.py #52

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Grace0114 opened this issue Nov 26, 2024 · 3 comments
Open

error about Line 123 and 419 in vcf2phylip.py #52

Grace0114 opened this issue Nov 26, 2024 · 3 comments

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@Grace0114
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error:
Traceback (most recent call last):
File "/media/test/data/qiuh/vcf2phylip.py", line 419, in
main()
File "/media/test/data/qiuh/vcf2phylip.py", line 123, in main
if line.startswith("#CHROM"):
TypeError: startswith first arg must be bytes or a tuple of bytes, not str

my vcf file:
#...
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CHBS015 CHBS016 CHBS017 CHBS018 ...
NW_025965004.1 8978 . A G . . . GT ./. 1/1 1/1 1/1 1/1 ./. 1/1 ...

@edgardomortiz
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Hi @Grace0114 ,

The snippet from your VCF doesn't tell me much, I need some actual lines from it to be able to diagnose the problem. Could you attach a few hundred genotype lines here?

Edgardo

@Grace0114
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Hi Edgardo
Thanks very much. I have solved this error by this method that I load the right zip file including vcf2phylip.py on the web github.com. Finally, I got merge.min4.phy.
Have a good day.
Grace

@edgardomortiz
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Hi @Grace0114 , I'm glad you were able to sort it out.

Edgardo

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