get_nested_taxa_for_names.py

#!/usr/bin/env python
"""uses a phlawd sqlite3 taxonomy database to retrieve all the names associated with each taxon 
in the provided list. <targetrank> specifies the rank of the taxa to be returned."""

if __name__ =='__main__':

    import sys, sqlite3

    if len(sys.argv) < 5:
        print("usage: get_nested_taxa_for_names.py <targetrank> <taxonnamesfile> <gbdb> <outfile>")
        sys.exit(0)

    target_rank = sys.argv[1].strip();

    higher_taxon_names = [s.strip() for s in open(sys.argv[2]).readlines()]

    conn = sqlite3.connect(sys.argv[3])
    c = conn.cursor()

    outfile = open (sys.argv[4],"w")
    outfile.write("higher_taxon,child_name\n")

    for name in higher_taxon_names:
        if len(name) > 0:
            print name
            results = c.execute("SELECT left_value, right_value FROM taxonomy WHERE name == ? ", (name,))
            res = c.fetchone()
            if (res != None):
                lval, rval = res
    #        print(lval, rval)
            else:
                print("Name " + name + " is not in the taxonomy")
                outfile.write(",".join([name,"(none)"]) +"\n")
                continue

            results = c.execute("SELECT name FROM taxonomy WHERE left_value > ? AND " + \
                "right_value < ? AND name_class == 'scientific name' AND node_rank == ?", (lval, rval, target_rank))

            for child_name in results.fetchall():
                outfile.write(",".join([name,child_name[0]]) +"\n")

    outfile.close()