def dumpResults(results, dir, prefix):
""" Print out the results {} in 4 files,
using this prefix & directory.
@parm results: {} w/ H1, H2, H12 {} and edge {} H1toH2.
@param dir: directory to put results, /w '/' at end.
@param prefix: name of file to stick before ex. '.H1'.
"""
utils_graph.dumpNodes(dir + prefix + '.H1', results['H1'])
utils_graph.dumpNodes(dir + prefix + '.H2', results['H2'])
utils_graph.dumpNodes(dir + prefix + '.H12', results['H12'])
utils_graph.dumpEdges(dir + prefix + '.H1toH2', results['H1toH2'])
else:
if check_gtr(elm, elm2freq):
f.write(elm + '\tGTR\n')
elif check_less(elm, elm2freq):
f.write(elm + '\tLESS\n')
else:
f.write(elm + '\tSAME\n')
# with open('mammal_bird.notTest', 'w') as f:
# for elm in utils_graph.intersectLists([control_elms,freq_elms]):
# if not elm in test_elms:
# if elm in elm2fracs:
# if check_gtr(elm, elm2fracs):
# f.write(elm + '\tGTR\n')
# elif check_less(elm, elm2fracs):
# f.write(elm + '\tLESS\n')
# else:
# f.write(elm + '\tSAME\n')
# else:
# if check_gtr(elm, elm2freq):
# f.write(elm + '\tGTR\n')
# elif check_less(elm, elm2freq):
# f.write(elm + '\tLESS\n')
# else:
# f.write(elm + '\tSAME\n')
utils_graph.dumpNodes('common_bird', utils_graph.intersectLists([elm2fracs,bird_elms]))
utils_graph.dumpNodes('common_mammal', utils_graph.intersectLists([elm2fracs,mammal_elms]))
ls = [human, swine, horse]
common_mammal, mammal_elms = get_common_elms(ls)
with open('mammalAll' + str(cut), 'w') as f:
for protein in common_mammal:
for elm in common_mammal[protein]:
f.write(protein + '\t' + elm + '\n')
ls = [chicken, duck]
common_bird, bird_elms = get_common_elms(ls)
with open('birdAll' + str(cut), 'w') as f:
for protein in common_bird:
for elm in common_bird[protein]:
f.write(protein + '\t' + elm + '\n')
use_mammal = get_unique_elms(common_mammal, common_bird)
use_bird = get_unique_elms(common_bird, common_mammal)
utils_graph.dumpNodes('mammal' + str(cut), use_mammal)
utils_graph.dumpNodes('bird' + str(cut), use_bird)
utils_graph.dumpNodes('common' + str(cut), common_all_elms)
ls = [human_controled, swine_controled,
horse_controled, chicken_controled, duck_controled]
common_all_controled, common_all_elms_controled = get_common_elms(ls)
ls = [human_controled, swine_controled, horse_controled]
common_mammal_controled, mammal_elms_controled = get_common_elms(ls)
with open('mammalAllControled' + str(cut), 'w') as f:
for protein in common_mammal_controled:
for elm in common_mammal_controled[protein]:
f.write(protein + '\t' + elm + '\n')
ls = [chicken_controled, duck_controled]
protein_ls = {}
new2old = {}
old2new = {}
old_fasta = utils_fasta.loadFASTA(sys.argv[1])
for protein in old_fasta.keys():
new_seq = clean(old_fasta[protein])
name = protein
if name.split('.')[-1] != vp_suffix:
name = name + '.' + vp_suffix
utils_fasta.prettyPrint(name, new_seq)
protein_ls[name] = True
new2old[name] = {}
old2new[name] = {}
new_index = 0
for old_index in xrange(len(old_fasta[protein])):
old_residue = old_fasta[protein][old_index]
if old_residue == '-' or old_residue == '*':
pass
else:
new2old[name][new_index+1] = old_index+1
old2new[name][old_index+1] = new_index+1
new_index += 1
f = open(new2old_file, 'w')
pickle.dump(new2old,f)
f.close()
f = open(old2new_file, 'w')
pickle.dump(old2new,f)
f.close()
utils_graph.dumpNodes(protein_ls_output_file, protein_ls)