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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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cannot extract snpfrom customed vcf #221

Open chengarthur opened 4 years ago

chengarthur commented 4 years ago

Hi I am trying to extract snp from my snp and I have used V2.1&2.2 bench, there is a same error.

cmdline： python hisat2_extract_snps_haplotypes_VCF.py "/media/wgs/reference/Homo_sapiens_assembly38.fasta" "/media/wgs/wgs_practice/joint_calling/1013clean.vcf.gz" snp

error： Traceback (most recent call last): File "hisat2_extract_snps_haplotypes_VCF.py", line 919, in args.verbose) File "hisat2_extract_snps_haplotypes_VCF.py", line 616, in main if line.startswith("##"): TypeError: startswith first arg must be bytes or a tuple of bytes, not str I tested db142 and my own vcf and the error is the same.

parkchanhee commented 4 years ago

Python scripts in HISAT2 works on python2. We have plans to change it to be compatible with python3.