#!/usr/bin/env python
import argparse
import os
import re
from rosetta_score_files import score2dict
parser = argparse.ArgumentParser()
parser.add_argument('-score_file', default=[x for x in os.listdir('./') if re.match('^(?!purple).*\.score', x)][0])
parser.add_argument('-n', default=5, type=int)
args = vars(parser.parse_args())
scores = score2dict(args['score_file'])
passed_scores = {v['ddg']: k for k, v in scores.items() if v['purple']}
sorted_scores = sorted(passed_scores.keys())
fout = open('extract_purples', 'wr+')
try:
print '\n'.join(passed_scores[sorted_scores[i]] for i in range(args['n']))
fout.write('\n'.join(passed_scores[sorted_scores[i]] for i in range(args['n'])))
except:
print 'found nothin'
fout.close()
def main():
"""
A script that takes a fasta and score files and assembles bins. a bin is a stack of
sequences that have similar AAs at the same positions (set by type_dict and
positions_dict respectively. each sequence is read, and it's score is examined whether
it passes my thresholds (purple). if it is it is assigned a bin, where only Negative
and Positive make a difference. the set of all generated bins (basically a list of
strings of n/p/c) is subsetted to get the longest subsets of bins that differe from
all other bins in their subset in at least 1 position N <> P.
INPUT: 1st cmd argument fasta file
2nd cmd argument score file
:return:
"""
import sys
from rosetta_score_files import score2dict
import operator
from collections import Counter
### this positions dict is for the 1st, 8 parts switches design
# positions_dict = {'1anu': [36, 38, 114, 115, 117, 120, 124, 126], '1ohz': [37, 39, 115, 116, 118, 121, 125, 127],
# '2ccl': [37, 39, 115, 116, 118, 121, 125, 127]}
### this positions dict if for the second, 10 parts switches design from 1-2.3.2015
positions_dict = {'1anu': [32, 36, 62, 65, 69, 82, 115, 126],
'1aoh': [33, 37, 63, 66, 70, 83, 119, 130],
'1ohz': [33, 37, 63, 66, 70, 83, 116, 127],
'2ccl': [33, 37, 63, 66, 70, 83, 116, 127]}
type_dict = {'D': 'n', 'E': 'n', 'K': 'p', 'R': 'p'}
scores = score2dict(sys.argv[2])
bins = {}
num_structs_bin = {}
f = open(sys.argv[1], 'r')
cont = f.read().split('>')
seq_dict = {i.split('\n')[0]: i.split('\n')[1] for i in cont if len(i) > 0}
for name, seq in seq_dict.items():
if scores[name]['purple']:
coh_name = name.split('_')[0]
switches = ''.join([type_dict[seq[i-1]] if seq[i-1] in type_dict.keys()
else 'c' for i in positions_dict[coh_name]])
### adding a condition where total #charges is <= 7, and distributes 5/2 or 4/3:
counter = Counter(switches)
if counter['n']+counter['p'] != 7 or counter['n'] < 2 or counter['p'] < 2:
continue
###
if switches not in bins.keys():
bins[switches] = []
num_structs_bin.update({switches: 0})
bins[switches].append(name)
num_structs_bin[switches] += 1
bin_subsets = bin_subsetter(bins.keys())
bin_subsets_struct = {i: [num_structs_bin[j] for j in bini] for i,bini in enumerate(bin_subsets)}
least_ones = 1000000
chosen_bsss = 'no bin subsets'
for bsss_key, bsss_val in bin_subsets_struct.items():
if len([i for i in bsss_val if i == 1]) < least_ones:
chosen_bsss = bsss_key
least_ones = len([i for i in bsss_val if i == 1])
best_bins_structs = []
for best_bin in bin_subsets[chosen_bsss]:
score_list = [scores[i] for i in bins[best_bin]]
score_list.sort(key=operator.itemgetter('ddg'))
best_bins_structs.append({best_bin: [i['description'] for i in score_list]})
for biner in best_bins_structs:
print biner.keys()[0].upper()
for struct in biner.values()[0]:
print struct
print '\n'
#!/usr/bin/env python
import argparse
import os
import re
from rosetta_score_files import score2dict
parser = argparse.ArgumentParser()
parser.add_argument('-score_file',
default=[
x for x in os.listdir('./')
if re.match('^(?!purple).*\.score', x)
][0])
parser.add_argument('-n', default=5, type=int)
args = vars(parser.parse_args())
scores = score2dict(args['score_file'])
passed_scores = {v['ddg']: k for k, v in scores.items() if v['purple']}
sorted_scores = sorted(passed_scores.keys())
fout = open('extract_purples', 'wr+')
try:
print '\n'.join(passed_scores[sorted_scores[i]] for i in range(args['n']))
fout.write('\n'.join(passed_scores[sorted_scores[i]]
for i in range(args['n'])))
except:
print 'found nothin'
fout.close()
