"""Find ELMs that are conserved on
mammal flu protiens for all
years and strains."""
import os, global_settings, utils_motif, utils
from collections import defaultdict
dir = 'working/Jul1_year'
birds = ('duck', 'chicken')
years = range(2000,2011,1)
strains = ('H9N2', 'H5N1')
utils.get_cons_elms(dir, birds, years, strains, '70')
for ELM sequences."""
import os, global_settings, utils_motif, utils, sys
from collections import defaultdict
out_file_elms = sys.argv[1]
out_file_seqs = sys.argv[2]
out_file_simpleELMseqs = sys.argv[3]
host = sys.argv[4] # bird|mammal
dir = "working/Jul7"
years = range(2000, 2011, 1)
if host == "mammal":
hosts = ("human",)
strains = ("H5N1",)
elif host == "bird":
hosts = ("chicken",)
strains = ("H5N1",)
d = {"ELM": True}
suffix = ".elms"
utils.get_cons_elms(dir, hosts, years, strains, "90", d, out_file_elms, suffix)
# d = {'ELMseq':True}
# suffix = '.elmseqs'
# utils.get_cons_elms(dir, hosts, years, strains, '70', d, out_file_seqs, suffix)
# d = {'ELMseq':True}
# suffix = '.simpleelmseqs'
# utils.get_cons_elms(dir, hosts, years, strains, '70', d, out_file_simpleELMseqs, suffix)
