import sys
from dp.associations import GeneAssociations
from dp.ontology import Ontology
from collections import Counter
from dp.utils import parseFasta
seqs = set()
names = set()
fastafile = open(sys.argv[1])
MIN_SEQ_LEN = 32
MAX_SEQ_UNK = 0.1
TAXONS_HOMMO_SAPIENS = {9606}
asoc = GeneAssociations.fromFile(sys.argv[2], taxons = TAXONS_HOMMO_SAPIENS)
ontology = Ontology(sys.argv[3])
ontology.setAssociations(asoc)
asoc.transitiveClosure()
associated = set()
for k,v in asoc.associations.items():
associated.update({g.upper() for g in v})
ss = dict(parseFasta("data/ss.txt"))
#print(associated)
for l in fastafile:
name, typ, *_ = l[1:].split(" ")
name = name.upper()
seq = next(fastafile)
sskey = "%s:secstr" % name.replace("_",":")
if typ != 'mol:protein' \
or len(seq) < MIN_SEQ_LEN \
import sys
from dp.associations import GeneAssociations
from dp.ontology import Ontology
from collections import Counter
from dp.utils import parseFasta
seqs = set()
names = set()
fastafile = open(sys.argv[1])
MIN_SEQ_LEN = 32
MAX_SEQ_UNK = 0.1
TAXONS_HOMMO_SAPIENS = {9606}
asoc = GeneAssociations.fromFile(sys.argv[2], taxons=TAXONS_HOMMO_SAPIENS)
ontology = Ontology(sys.argv[3])
ontology.setAssociations(asoc)
asoc.transitiveClosure()
associated = set()
for k, v in asoc.associations.items():
associated.update({g.upper() for g in v})
ss = dict(parseFasta("data/ss.txt"))
#print(associated)
for l in fastafile:
name, typ, *_ = l[1:].split(" ")
name = name.upper()
seq = next(fastafile)
sskey = "%s:secstr" % name.replace("_", ":")
if typ != 'mol:protein' \
or len(seq) < MIN_SEQ_LEN \
