CB513 | CB513 results | User Interface library

import os 

import sys

import numpy as np

from proteinss import ProteinSS

map_dssp_3_alphabet = {"H":1,"I":1,"G":1,"E":2,"B":2,"T":3,"S":3, "_":3, "?":3}
map_dssp_8_alphabet = {"H":1,"I":2,"G":3,"E":4,"B":5,"T":6,"S":7, "_":8, "?":8}

def extract_file(ss_file):
    print ("Extracting :"), ss_file

fi = open(ss_file, 'rU')
seq_string = ""
ss_string  = ""
alignments = []
for line in fi:
    if line.startswith("RES:"):
       seq_string = line.split(":")[1].rstrip('\n')

    if line.startswith("DSSP:"):
       ss_string = line.split(":")[1].rstrip('\n')

    if line.startswith("align"):
       alignment = line.split(":")[1].rstrip('\n')
       alignments.append( alignment.split(",")[0:-1] )

seq_l = seq_string.split(",")[0:-1]
ss_l  = ss_string.split(",")[0:-1]

prot = ProteinSS(seq_l, ss_l)

for al_ in alignments:
    prot.add_alignment(al_)

return prot


def prepare_db(cb513_path, db_ofile, db_classes, wsize, alphabet):
    fo1 = open(db_ofile, 'w')
    fo2 = open(db_classes, 'w')


for root, dirs, files in os.walk(cb513_path):
    for name in files:
        if name.endswith(( ".all" )):
            ss_file = root + "/" + name
            prot = extract_file ( ss_file )
            if prot.is_valid():
                s1, s2 = prot.get_db_strings(wsize, map_dssp_3_alphabet, True)
                fo1.write(s1)
                fo2.write(s2)

fo1.close()
fo2.close()


if __name__ == "__main__":
    cb513_path = '../data/CB513'
    classes_ofile   = "../data/db/ss_a3.dat" 

window_width = int( sys.argv[5] ) 
db_ofile = "../data/db/aa_w" + str(window_width) + "_a3.dat"

if sys.argv[2] == "3":
    alphabet = map_dssp_3_alphabet
elif sys.argv[2] == "8":
    alphabet = map_dssp_8_alphabet
else:
    print ("Alphabet not recognized: choose between 3 or 8")
    sys.exit(1)

pubs_data = prepare_db(cb513_path, db_ofile, classes_ofile, window_width, alphabet)