sequence_locator: internal use case

[ArtPoon]

This is a Python script I used to batch process a FASTA file within Python:

from poplars.sequence_locator import *
from poplars.common import *
import sys

fasta = convert_fasta(open(sys.argv[1]))

virus = 'hiv'
base = 'NA'

configs = handle_args(virus, base)
ref_nt_seq, ref_aa_seq = configs[0][0][1], configs[1]
nt_coords = configs[2]
reference_sequence = configs[3]
nt_coords_handle = open(nt_coords, 'r')

ref_genome = Genome(virus, nt_coords_handle, ref_nt_seq, ref_aa_seq,
                    reference_sequence, base)

for h, s in fasta:
    query_seq = get_query(base, s, False)
    query = Query(base, ref_genome, query_sequence=query_seq)
    left, right = query.qcoords
    sys.stdout.write('{}\t{}\t{}\n'.format(h, left, right))

Some of this is unnecessarily complicated, such as setting up the Genome object. Ideally the workflow would look more like this:

from poplar import sequence_locator as locator

handle = open(sys.argv[1])
for h, s in convert_fasta(handle):
    result = locator(s, base='NT', virus='hiv')
    sys.stdout.write('{}\t{}\t{}\n'.format(h, result.left, result.right))