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 = []