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"]
