def do_import(orglistfn, scoredir, cpddir, treefn, outdir):
#copy tree.cpds and org_list.backup to target dir
#?
shutil.copy("/users/jianhou/work/model/model_training/tree_cpds/%s" % (common.TREE_CPD_FILE), "%s/%s" % (outdir, common.TREE_CPD_FILE))
shutil.copy(orglistfn, "%s/%s" % (outdir, common.ORGANISM_LIST_FILE))
org_abbr, org_long = common.read_organisms(outdir)
import_scores(org_abbr, scoredir, outdir)
import_cpds(cpddir, outdir)
import_tree(treefn, outdir)
def do_import(orglistfn, scoredir, cpddir, treefn, outdir, treecpd):
#copy tree.cpds and org_list.backup to target dir
#?
try:
shutil.copy(treecpd, "%s/%s" % (outdir, common.TREE_CPD_FILE))
shutil.copy(orglistfn, "%s/%s" % (outdir, common.ORGANISM_LIST_FILE))
org_abbr, org_long = common.read_organisms(outdir)
import_scores(org_abbr, scoredir, outdir)
import_cpds(cpddir, outdir)
import_tree(treefn, outdir)
except Exception:
print traceback.print_exc()
#!/usr/bin/env python
import sys, os, datetime
import common
ddir = sys.argv[1] # project dir
scoredir = sys.argv[2] # dir with .ecscores
o = open("%s/%s" % (ddir, common.FULL_REACTION_SCORE_FILE), "w")
rscores, ecs = common.read_scores(ddir)
org_abbr, org_long = common.read_organisms(ddir)
fns = os.listdir(scoredir)
scores = {}
for fn in fns:
if fn.endswith(".ecscores"):
org = org_abbr[fn[:-len(".ecscores")]]
scores[org] = {}
f = open("%s/%s" % (scoredir, fn))
for s in f:
if s.startswith("#"):
continue
ec, bs, bs1, bs2, gs, gs1, gs2 = s.strip().split("\t")
scores[org][ec] = (bs, bs1, bs2, gs, gs1, gs2)
ecs.add(ec)
keys = set(rscores.keys())
#return set() keys with adding set(scores.keys())
keys.update(set(scores.keys()))
keys = list(keys)
#!/usr/bin/env python
import sys, os, datetime
import common
ddir = sys.argv[1] # project dir
scoredir = sys.argv[2] # dir with .ecscores
o = open("%s/%s" % (ddir, common.FULL_REACTION_SCORE_FILE), "w")
rscores, ecs = common.read_scores(ddir)
org_abbr, org_long = common.read_organisms(ddir)
fns = os.listdir(scoredir)
scores = {}
for fn in fns:
if fn.endswith(".ecscores"):
org = org_abbr[fn[:-len(".ecscores")]]
scores[org] = {}
f = open("%s/%s" % (scoredir, fn))
for s in f:
if s.startswith("#"):
continue
ec, bs, bs1, bs2, gs, gs1, gs2 = s.strip().split("\t")
scores[org][ec] = (bs, bs1, bs2, gs, gs1, gs2)
ecs.add(ec)
keys = set(rscores.keys())
#return set() keys with adding set(scores.keys())
keys.update(set(scores.keys()))
keys = list(keys)
