gwctcore.logCheck(l, logfilename, gwctcore.getTime() + " | Starting codeml runs...\n");
if v == 0:
codeml_logfile = os.path.join(script_outdir, "codeml.log");
ctlfilename = "codeml.ctl";
i = 0;
numbars = 0;
donepercent = [];
for each in filelist:
if each.find(".fa") == -1:
continue;
if v == 0 and fileflag == 0:
numbars, donepercent = gwctcore.loadingBar(i, len(filelist), donepercent, numbars);
i = i + 1;
if fileflag == 1:
infilename = each;
else:
infilename = os.path.join(indir, each);
gid = each[:each.index(".")];
run_outdir = os.path.join(outdir, gid);
if not os.path.exists(run_outdir):
os.system("mkdir " + run_outdir);
if prune == 1:
seqs = gwctcore.fastaGetDict(infilename);
to_prune = [];
td, tree, r = gt.treeParse(open(treefile, "r").read().replace("\n",""),0);
tips = [node for node in td if td[node][2] == 'tip'];
# Read tree info for pruning
gc.printWrite(logfilename, gc.getTime() + " | Starting codeml runs...\n");
if v == 0:
codeml_logfile = os.path.join(outdir, "codeml.stdout");
ctlfilename = "codeml.ctl";
i, numbars, donepercent, numfiles = 0, 0, [], len(filelist);
# Loading bar stuff
fa_skip = [];
for cur_file in filelist:
if v == 0:
numbars, donepercent = gc.loadingBar(i, numfiles, donepercent, numbars);
i += 1;
if not cur_file.endswith(".fa"):
fa_skip.append(cur_file);
continue;
infilename = os.path.join(indir, cur_file);
gid = cur_file[:cur_file.index(".fa")];
run_outdir = os.path.join(codemldir, gid);
if not os.path.exists(run_outdir):
os.system("mkdir " + run_outdir);
if prune == 1:
seqs = gc.fastaGetDict(infilename);
to_prune = [tip for tip in tips if (">" + tip) not in seqs];
filelist = os.listdir(indir);
numfiles = len(filelist);
numbars = 0;
donepercent = [];
i = 0;
numsubs = 0;
numgenes = 0;
for each in filelist:
if each.find(".fa") == -1:
continue;
gflag = 0;
numbars, donepercent = gwctcore.loadingBar(i, numfiles, donepercent, numbars);
i = i + 1;
infilename = os.path.join(indir, each);
inseqs = gwctcore.fastaGetDict(infilename);
# print infilename;
seqlen = len(inseqs[">" + targets[0]]);
fid = each[:each.index(".fa")];
gid = "_".join(fid.split("_")[:2]);
chrome = fid[fid.find("chr"):fid.find("chr")+4]
for x in range(len(inseqs[">" + targets[0]])):
site = [];
target_alleles = [];
filelist = os.listdir(indir)
numfiles = len(filelist)
numbars = 0
donepercent = []
i = 0
numsubs = 0
numgenes = 0
for each in filelist:
if each.find(".fa") == -1:
continue
gflag = 0
numbars, donepercent = gwctcore.loadingBar(i, numfiles, donepercent,
numbars)
i = i + 1
infilename = os.path.join(indir, each)
inseqs = gwctcore.fastaGetDict(infilename)
# print infilename;
seqlen = len(inseqs[">" + targets[0]])
fid = each[:each.index(".fa")]
gid = "_".join(fid.split("_")[:2])
chrome = fid[fid.find("chr"):fid.find("chr") + 4]
for x in range(len(inseqs[">" + targets[0]])):
site = []
target_alleles = []
