# -*- coding: utf-8 -*-

# <nbformat>3.0</nbformat>

# <codecell>

import os, os.path

import sys

sys.path.append('/home/will/PySeqUtils/')

os.chdir('/home/will/PySeqUtils/')

from GeneralSeqTools import fasta_reader

import csv

# <codecell>

from HIVTransTool import map_seqs_to_ref, process_seqs

import csv

ref_path = 'HIVDBFiles/HXB2Sequence.fasta'

cor_res = {}

with open('TestData/test_mapping.csv') as handle:

for row in csv.DictReader(handle, delimiter='\t'):

cor_res[row['SeqName']] = (int(row['GenomeStart']), int(row['GenomeStop']))

with open('TestData/testSeqs.fasta') as handle:

input_seqs = list(fasta_reader(handle))

#with open('/home/will/HIVRate/hiv-db.fasta') as handle:

# seqs = list(fasta_reader(handle))

# <codecell>

from itertools import product

list(product('abcdefg', range(5)))

# <codecell>

fields = ['Name','RegionName', 'QueryNucStart','QueryNucStop','QueryNuc',

'RegionNucStart','RegionNucStop','RegionAAStart', 'RegionAAStop', 'QueryAA']

with open('TestData/LocatorRes.tsv', 'w') as handle:

writer = csv.DictWriter(handle, fields, delimiter='\t')

writer.writeheader()

for row in process_seqs(input_seqs, extract_regions = True):

writer.writerow(row)

#print row

#raise KeyError

# <codecell>

import csv

headers = ['Name', 'RegionName', 'QueryNucStart', 'QueryNucStop', 'QueryNuc',

'RegionNucStart', 'RegionNucStop', 'RegionAAStart','RegionAAStop','QueryAA']

with open('test_output.tsv', 'w') as handle:

writer = csv.DictWriter(handle, headers, delimiter='\t')

found_pats = set()

for num, row in enumerate(process_seqs(seqs)):

found_pats.add(row['Name'])

if (num == 1) or (num == 100) or (num == 1000) or (num % 5000 == 0):

print num, len(found_pats)

writer.writerow(row)

# <codecell>

len(seqs)

# <codecell>