dindex = i print "ML td", l_umtd, l_mmtd else: umtd1 = t1 mmtd1 = t2 break return [dindex, td, umtd1, mmtd1] ################################ # # main: # points = None if False != argParser.getOptionalArg("--saved"): fin = open( argParser.getOptionalArg("--saved"), "r") [points, t1lnls, t2lnls, t1trees, t2trees] = pickle.load( fin ) fin.close() else: [t1trees, t1lnls] = return_trees_from_trace(t1path) [t2trees, t2lnls] = return_trees_from_trace(t2path) write_all_trees(t1trees, t2trees) write_trace(t1trees, t1lnls, t1path + ".unique.txt") write_trace(t2trees, t2lnls, t2path + ".unique.txt") points = build_distance_matrix(t1trees, t2trees) fout = open("points.txt", "w") pickle.dump([points, t1lnls, t2lnls, t1trees, t2trees], fout) fout.close() draw_heatmap(points, t1lnls, t2lnls, "compare_phyml_tree_traces")
return "XVII" if x == 18: return "XVIII" if x == 19: return "XIX" if x == 20: return "XX" return None tabpath = ap.getArg("--in") if False == os.path.exists(tabpath): print "\n. I cannot find your TAB file at", tabpath exit() gffpath = ap.getOptionalArg("--out") if gffpath == False or gffpath == None: gffpath = tabpath + ".gff" fin = open(tabpath, "r") fout = open(gffpath, "w") fout.write("# gff-version 3\n") fout.write("# This file was auto-generated by the script tab2gff.py\n") fout.write("# using data from the TAB file " + tabpath + "\n") fout.write("#\n") for l in fin.xreadlines(): if l.startswith("#"): continue tokens = l.split() genename = tokens[0]
command = "tar czf results.tar.gz " for f in files: if os.path.exists(f): command += f + " " os.system(command) print "\n. Results are packaged into results.tar.gz" ###################################################################### # # main # splash() """If the user gives a configpath, then it's referenced data will be imported into the database.""" configpath = ap.getOptionalArg("--configpath") if configpath != False: ap.params = read_config( configpath ) if False == validate_config(ap.params): print "\n. Error: something is wrong with your configuration file." print ". Look at previous errors for more detail." exit(0) """If the user didn't give a configpath, then we at least need a dbpath (to load a prior database).""" dbpath = ap.getOptionalArg("--dbpath") if configpath == False: print "\n. Error, you need to specify a configuration path, using --configpath"
# output: a CRAN script and a PDF plot (generated from the CRAN script) # # import math import os import re import sys from dendropy import Tree from argParser import ArgParser argParser = ArgParser(sys.argv) t1path = sys.argv[1] t2path = sys.argv[2] id = argParser.getOptionalArg("--id") if id == False: id = "" import numpy as np import cogent.maths.stats.test as stats colors = ["orangered","royalblue", "black"] pch = [20,5,3] COLORS = {} COLORS["unimax"] = "tomato" COLORS["multimax"] = "deepskyblue" COLORS["true"] = "black" COLORS["bionj"] = "snow3" # set is an array of floats
command = "tar czf results.tar.gz " for f in files: if os.path.exists(f): command += f + " " os.system(command) print "\n. Results are packaged into results.tar.gz" ###################################################################### # # main # splash() """If the user gives a configpath, then it's referenced data will be imported into the database.""" configpath = ap.getOptionalArg("--configpath") if configpath != False: ap.params = read_config(configpath) if False == validate_config(ap.params): print "\n. Error: something is wrong with your configuration file." print ". Look at previous errors for more detail." exit(0) """If the user didn't give a configpath, then we at least need a dbpath (to load a prior database).""" dbpath = ap.getOptionalArg("--dbpath") if configpath == False: print "\n. Error, you need to specify a configuration path, using --configpath" exit()
print "\t\treplicates conditions, and species." print "" print "======================================================================" splash() """read_cli reads the command-line, the annotation file, and creates a SQLite3 database.""" con = read_cli(ap) print_settings(con) validate_configuration_import(con) if ap.getOptionalToggle("--load_db_only"): "\n. Ending" exit() """Jump allows for some steps to be skipped.""" jump = ap.getOptionalArg("--jump") stop = ap.getOptionalArg("--stop") if jump == False: jump = 0 else: jump = float(jump) if stop == False: stop = 10000000 else: stop = float(stop) """Run Bowtie2 for each FASTQ path""" if jump <= 1 and stop > 1: run_bowtie(con)
from Bio import SeqIO from chipseqdb import * from chipseqdb_api import * from argParser import ArgParser ap = ArgParser(sys.argv) from plot_scatter import * """Jump allows for some steps to be skipped.""" jump = ap.getOptionalArg("--jump") stop = ap.getOptionalArg("--stop") if jump == False: jump = 0 else: jump = float(jump) if stop == False: stop = 10000000 else: stop = float(stop) def read_motifs(motif_path): """Reads PSWM data from a text file. Motifs are expected to look like this: /NAME=[SWISS] ABF1 TYPE=PSFM SPECIES=S.cer 0.208782 0.155386 0.135415 0.500414 0.745936 0.0 0.254063 0.0 0.0 0.0 0.0 1.0
import re from map_anc_2_anc import * from argParser import ArgParser ap = ArgParser(sys.argv) anc1 = ap.getArg("--anc1") nick1 = ap.getArg("--nick1") msa1 = ap.getArg("--msa1") seed1 = ap.getArg("--seed1") anc2 = ap.getArg("--anc2") nick2 = ap.getArg("--nick2") msa2 = ap.getArg("--msa2") seed2 = ap.getArg("--seed2") runid = ap.getOptionalArg("--runid") if runid == False: exit() rsitesa = [] x = ap.getOptionalList("--restrict_sites_1") if x != None: for s in x: rsitesa.append( int(s) ) rsitesb = [] x = ap.getOptionalList("--restrict_sites_2") if x != None: for s in x: rsitesb.append( int(s) ) colors = ["blue", "red", "orange", "green", "black"]
import re from map_anc_2_anc import * from argParser import ArgParser ap = ArgParser(sys.argv) anc1 = ap.getArg("--anc1") nick1 = ap.getArg("--nick1") msa1 = ap.getArg("--msa1") seed1 = ap.getArg("--seed1") anc2 = ap.getArg("--anc2") nick2 = ap.getArg("--nick2") msa2 = ap.getArg("--msa2") seed2 = ap.getArg("--seed2") runid = ap.getOptionalArg("--runid") if runid == False: exit() rsitesa = [] x = ap.getOptionalList("--restrict_sites_1") if x != None: for s in x: rsitesa.append(int(s)) rsitesb = [] x = ap.getOptionalList("--restrict_sites_2") if x != None: for s in x: rsitesb.append(int(s)) colors = ["blue", "red", "orange", "green", "black"]