augur.io.vcf

augur.io.vcf.is_vcf(filename)

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.read_vcf(filename)

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)