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)