INNER CODE UNIT · Python

main

StaPH-B/docker-builds · build-files/cbird-util/2.0/est_coverage.py:13

def main(args):
    total_bases = args.total_bases
    top_taxid = args.top_taxid
    alt_gs = args.alt_gs
    genome_length = args.genome_length

    # read assembly stats file
    gs_df = pd.read_csv("/usr/local/lib/species_genome_size.txt", sep = '\t')
    
    ## Coverage ##
    # get total base number
    with open(total_bases, "r") as tb:
        lines = tb.readlines()    
    basenum = lines[0]
    basenum_trim = lines[1]

    # find top hit's expected genome size
    x = gs_df.loc[gs_df ["#species_taxid"]==int(top_taxid), "expected_ungapped_length"]

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