#!/usr/bin/env python

import csv

import os

import sys

from opener import opener

import utils

from Searcher import Searcher

values = {}

variables = ['found_strings', 'evalue', 'ali_from', 'ali_to', 'vd_insertion_length', 'dj_insertion_length']

for var in variables:

values[var] = {}

for region in utils.regions:

values[var][region] = {}

for imatch in range(3):

values[var][region][imatch] = []

assert len(sys.argv) == 3;

data_type = sys.argv[1]

human = sys.argv[2]

# for human in A B C; do

# datadir=data/human-beings/$human/M/data

# bzgrep -m100 . $datadir/data.tsv.bz2 | sed 's/[ \t][ \t]*/,/g'|cut -f2 -d, |sed 's/nucleotide/seq/'> $datadir/head-data.csv

# done

naivety = 'M'

infname = ''

if data_type == 'simu':

infname = '/home/dralph/Dropbox/work/recombinator/output/' + human + '/' + naivety + '/simu.csv'

else:

infname = 'data/human-beings/' + human + '/' + naivety + '/' + data_type + '/head-data.csv'

baseoutdir = 'data/human-beings/' + human + '/' + naivety + '/' + data_type

print 'opening ',infname

print ' output',baseoutdir

with opener('r')(infname) as infile:

germlines = utils.read_germlines('../../../recombinator')

reader = csv.DictReader(infile)

il = 0

for inline in reader:

il += 1

print inline['seq'][-100:]

# if len(inline['seq']) != 130:

# assert 'simulated' in infname

searcher = Searcher(inline['seq'][-100:], debug=False, n_matches_max=5)

found_str = searcher.search()

values['found_strings']['v'][0].append(found_str) # toss them in ['v'][0] -- doesn't really make sense, but they're fine anywhere

if found_str != 'vjd': # skip the ones where we didn't find matches in this order (see freqs above).

continue

for region in utils.regions:

for imatch in range(len(searcher.matches[region])):

if imatch > 2:

break

match = searcher.matches[region][imatch]

if imatch == 0 and region == 'd':

# print '%s (%3d%3d) --> (%3d%3d %s)' % (region, match['ali_from'], match['ali_to'], match['ali_from'] - 1, len(searcher.query_seqs[region]) - match['ali_to'], searcher.query_seqs[region]),

values['vd_insertion_length'][region][imatch].append(match['ali_from'] - 1) # NOTE these are index *one* counting (!!!)

values['dj_insertion_length'][region][imatch].append(len(searcher.query_seqs[region]) - match['ali_to']) # NOTE these are index *one* counting (!!!)

values['evalue'][region][imatch].append(match['evalue'])

values['ali_from'][region][imatch].append(match['ali_from'])

values['ali_to'][region][imatch].append(match['ali_to'])

# if il > 100:

# sys.exit()

# print ''

# break

for region in utils.regions:

for var in variables:

outdir = baseoutdir + '/' + var

if not os.path.exists(outdir):

os.makedirs(outdir)

for imatch in range(len(searcher.matches[region])):

if imatch > 2:

break

with opener('w')(outdir + '/' + region + '-' + str(imatch) + '.txt') as outfile:

for value in values[var][region][imatch]:

if var == 'found_strings':

outfile.write('%s\n' % value)

else:

outfile.write('%7e\n' % value)