"""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)