Contents

require 'snp-search'

#path for embl file here
genome_sequence = Bio::FlatFile.open(Bio::EMBL, "path_for_embl_file_here").next_entry

#path for vcf file here
vcf_mpileup_file = "path_for_vcf_file_here"

#array of strain names here
strains = ["STRAIN_NAME_1", "STRAIN_NAME_2"]

# Thats it, you job is done here.

# The populate_strains method populates the strains in the db. It uses the strain names in array.
populate_strains(strains)

# The populate_features_and_annotations method populates the features and annotations.  It uses the embl/gbk file.
populate_features_and_annotations(genome_sequence)

# The populate_snps_alleles_genotypes method populates the snps, alleles and genotypes.  It uses the strain names (array) and vcf file.
populate_snps_alleles_genotypes(strains, vcf_mpileup_file)

Version data entries

1 entries across 1 versions & 1 rubygems

Version	Path
snp-search-0.2.0	lib/user_entry_file.rb