Convenience method to check if a file is a vcf file.
>>> is_vcf(None) False >>> is_vcf("./foo") False >>> is_vcf("./foo.vcf") True >>> is_vcf("./foo.vcf.GZ") True
- augur.io.vcf.write_VCF_translation(prot_dict, vcf_file_name, ref_file_name)
Writes out a VCF-style file (which seems to be minimally handleable by vcftools and pyvcf) of the AA differences between sequences and the reference. This is a similar format created/used by read_in_vcf except that there is one of these dicts (with sequences, reference, positions) for EACH gene.
Also writes out a fasta of the reference alignment.
EBH 12 Dec 2017
- augur.io.vcf.write_vcf(input_filename, output_filename, dropped_samps)