def runSeqGen(workingFile, srp_hap_file, srp_tree_file, debug):
seqgen_infile = workingFile + "_seqgen.phylip"
seqgen = runExtProg(seqgenDir + "./seq-gen", pdir=seqgenDir, length=3)
seqgen.set_param_at("-mHKY", 1)
seqgen.set_param_at("-t2", 2)
seqgen.set_param_at("-k1", 3)
# seqgen.set_param_at("-d0.1", 4)
# seqgen.set_param_at("-s0.00001", 4)
seqgen.set_stdin(seqgen_infile)
all_unique = False
repeat = 0
while not all_unique:
if repeat == 100:
runBSSC(workingFile, srp_tree_file, debug)
print "==========rerun BSSC========"
repeat = 0
repeat += 1
# print repeat
seqgen.run(0)
all_unique = check_unique_sequences(seqgen)
temp_handle = open(workingFile + "_seqgen_out.phylip", "w")
temp_handle.write(seqgen.output)
temp_handle.close()
SeqIO.convert(workingFile + "_seqgen_out.phylip", "phylip",
workingFile + ".fasta", "fasta")
shutil.copy(workingFile + ".fasta", srp_hap_file)
def runSeqGen(workingFile, srp_hap_file, srp_tree_file, debug):
seqgen_infile = workingFile + "_seqgen.phylip"
seqgen = runExtProg(seqgenDir + "./seq-gen", pdir=seqgenDir, length=3)
seqgen.set_param_at("-mHKY", 1)
seqgen.set_param_at("-t2", 2)
seqgen.set_param_at("-k1", 3)
# seqgen.set_param_at("-d0.1", 4)
# seqgen.set_param_at("-s0.00001", 4)
seqgen.set_stdin(seqgen_infile)
all_unique = False
repeat = 0
while not all_unique:
if repeat == 100:
runBSSC(workingFile, srp_tree_file, debug)
print "==========rerun BSSC========"
repeat = 0
repeat += 1
# print repeat
seqgen.run(0)
all_unique = check_unique_sequences(seqgen)
temp_handle = open(workingFile + "_seqgen_out.phylip", "w")
temp_handle.write(seqgen.output)
temp_handle.close()
SeqIO.convert(workingFile + "_seqgen_out.phylip", "phylip", workingFile + ".fasta", "fasta")
shutil.copy(workingFile + ".fasta", srp_hap_file)
def runSam2Fasta(workingFile,
result_file_prefix,
samfile_prefix,
srp_read_prefix,
error_free_model=True,
debug=False):
reference_file = workingFile + ".cons"
srp_temp_file = workingFile + "_temp.fasta"
sam_outfile = workingFile + samfile_prefix + ".sam"
# sam2fasta = runExtProg(softwareDir + "./sam2fasta.py", length=3)
sam2fasta = runExtProg("./sam2fasta_mod.py", length=3)
sam2fasta.set_param_at(reference_file, 1)
sam2fasta.set_param_at(sam_outfile, 2)
sam2fasta.set_param_at(srp_temp_file, 3)
sam2fasta.run(debug)
shutil.copy(sam_outfile, result_file_prefix + samfile_prefix + ".sam")
shutil.copy(
srp_temp_file,
result_file_prefix + srp_read_prefix + samfile_prefix + ".fasta")
if error_free_model:
sam_outfile = workingFile + samfile_prefix + "_errFree.sam"
sam2fasta.set_param_at(sam_outfile, 2)
sam2fasta.run(debug)
shutil.copy(sam_outfile,
result_file_prefix + samfile_prefix + "_errFree.sam")
shutil.copy(
srp_temp_file, result_file_prefix + srp_read_prefix +
samfile_prefix + "_errFree.fasta")
def runBSSC(workingFile, srp_tree_file, debug):
bssc = runExtProg(bsscDir + "BSSC_original", pdir=bsscDir, length=3)
bssc.set_param_at("-f", 1)
bssc.set_param_at(workingFile + "_BSSC.par", 2)
bssc.set_param_at(1, 3)
bssc_paup_result = workingFile + "_BSSC.paup"
# bssc_tree_result = workingFile + "_true_trees.trees"
try:
os.remove(bssc_paup_result)
# os.remove(workingFile + "_0.pau")
except OSError:
pass
while not os.path.exists(bssc_paup_result):
bssc.run()
# input_handle = open(bssc_tree_result, "rU")
input_handle = open(bssc_paup_result, "rU")
for line in input_handle:
if line.find("tree true_tree_1") > 0:
line = line.strip()
start = line.index("U]") + 3
treeString = line[start:]
tree = Phylo.read(StringIO(treeString), 'newick')
input_handle.close()
for clade in tree.find_clades():
if clade.name:
match = re.match(MATCH_TREE_NODE, clade.name)
if match:
index = match.group(2)
clade.name = "hap_" + str(int(index) - 1)
input_handle = open(bssc_paup_result, "rU")
sequences = AlignIO.read(input_handle, "nexus")
input_handle.close()
seq = sequences[0]
ref_handle = open(workingFile + ".cons", "w")
ref_handle.write(">%s\n%s\n" % ("Ref", seq.seq))
ref_handle.close()
output_handle = open(workingFile + "_seqgen.phylip", "w")
output_handle.write("1 1200\n")
output_handle.write("%s %s\n" % ("ancestor", seq.seq))
output_handle.write("1\n")
Phylo.write(tree, output_handle, "newick")
output_handle.close()
output_handle = open(srp_tree_file, "w")
Phylo.write(tree, output_handle, "newick")
output_handle.close()
def runBSSC(workingFile, srp_tree_file, debug):
bssc = runExtProg(bsscDir + "BSSC_original", pdir=bsscDir, length=3)
bssc.set_param_at("-f", 1)
bssc.set_param_at(workingFile + "_BSSC.par", 2)
bssc.set_param_at(1, 3)
bssc_paup_result = workingFile + "_BSSC.paup"
# bssc_tree_result = workingFile + "_true_trees.trees"
try:
os.remove(bssc_paup_result)
# os.remove(workingFile + "_0.pau")
except OSError:
pass
while not os.path.exists(bssc_paup_result):
bssc.run()
# input_handle = open(bssc_tree_result, "rU")
input_handle = open(bssc_paup_result, "rU")
for line in input_handle:
if line.find("tree true_tree_1") > 0:
line = line.strip()
start = line.index("U]") + 3
treeString = line[start:]
tree = Phylo.read(StringIO(treeString), 'newick')
input_handle.close()
for clade in tree.find_clades():
if clade.name:
match = re.match(MATCH_TREE_NODE, clade.name)
if match:
index = match.group(2)
clade.name = "hap_" + str(int(index) - 1)
input_handle = open(bssc_paup_result, "rU")
sequences = AlignIO.read(input_handle, "nexus")
input_handle.close()
seq = sequences[0]
ref_handle = open(workingFile + ".cons", "w")
ref_handle.write(">%s\n%s\n" % ("Ref", seq.seq))
ref_handle.close()
output_handle = open(workingFile + "_seqgen.phylip", "w")
output_handle.write("1 1200\n")
output_handle.write("%s %s\n" % ("ancestor", seq.seq))
output_handle.write("1\n")
Phylo.write(tree, output_handle, "newick")
output_handle.close()
output_handle = open(srp_tree_file, "w")
Phylo.write(tree, output_handle, "newick")
output_handle.close()
def runShrimp(workingFile, shrimp_infile_prefix, shrimp_prefix, debug):
reference_file = workingFile + ".cons"
shrimp_infile = workingFile + shrimp_infile_prefix
sam_outfile = workingFile + shrimp_prefix + ".sam"
shrimp = runExtProg(shrimpDir + "gmapper-ls", length=3)
shrimp.set_param_at(shrimp_infile, 1)
shrimp.set_param_at(reference_file, 2)
shrimp.set_param_at("-h 25%", 3)
shrimp.add_switch("--qv-offset 33") # # for ART output
# shrimp.add_switch("--ignore-qvs")
# shrimp.set_param_at("-P", 3)
shrimp.run(debug)
outfile_handle = open(sam_outfile, "w")
outfile_handle.write(shrimp.output)
def runMetaSim(workingFile, workingDir, debug):
metaSim_infile = workingFile + ".fasta"
if os.path.exists(workingFile + "-454.fna"):
os.remove(workingFile + "-454.fna")
metaSim = runExtProg(metaSimDir + "./MetaSim", pdir=metaSimDir, length=9)
metaSim.set_param_at("cmd", 1)
metaSim.set_param_at("--454", 2)
metaSim.set_param_at("-f250", 3)
metaSim.set_param_at("-t25", 4)
metaSim.set_param_at("-r2000", 5)
metaSim.set_param_at("-c", 6)
metaSim.set_param_at("-d", 7)
metaSim.set_param_at(workingDir, 8)
metaSim.set_param_at(metaSim_infile, 9)
metaSim.run(debug)
def runShrimp(workingFile, shrimp_infile_prefix, shrimp_prefix, debug):
reference_file = workingFile + ".cons"
shrimp_infile = workingFile + shrimp_infile_prefix
sam_outfile = workingFile + shrimp_prefix + ".sam"
shrimp = runExtProg(shrimpDir + "gmapper-ls", length=3)
shrimp.set_param_at(shrimp_infile, 1)
shrimp.set_param_at(reference_file, 2)
shrimp.set_param_at("-h 25%", 3)
shrimp.add_switch("--qv-offset 33") # # for ART output
# shrimp.add_switch("--ignore-qvs")
# shrimp.set_param_at("-P", 3)
shrimp.run(debug)
outfile_handle = open(sam_outfile, "w")
outfile_handle.write(shrimp.output)
def runART(workingFile, art_output_prefix, error_free_model=True, debug=False):
art_infile = workingFile + ".fasta"
art = runExtProg(artDir + "./art_illumina", pdir=artDir)
art.set_param_at("-sam", 1)
art.add_switch("-i %s" % art_infile)
art.add_switch("-l 75")
art.add_switch("-f 20")
art.add_param("-o %s%s" % (workingFile, art_output_prefix))
if error_free_model:
art.add_switch("-ef")
# art.add_param("-na")
# print art.get_extract_switch()
# art.set_param_at("-c", 6)
# art.set_param_at("-d", 7)
# art.set_param_at(workingDir, 8)
# art.set_param_at(art_infile, 9)
art.run(debug)
def runART(workingFile, art_output_prefix, error_free_model=True, debug=False):
art_infile = workingFile + ".fasta"
art = runExtProg(artDir + "./art_illumina", pdir=artDir)
art.set_param_at("-sam", 1)
art.add_switch("-i %s" % art_infile)
art.add_switch("-l 75")
art.add_switch("-f 20")
art.add_param("-o %s%s" % (workingFile, art_output_prefix))
if error_free_model:
art.add_switch("-ef")
# art.add_param("-na")
# print art.get_extract_switch()
# art.set_param_at("-c", 6)
# art.set_param_at("-d", 7)
# art.set_param_at(workingDir, 8)
# art.set_param_at(art_infile, 9)
art.run(debug)
def runMetaSim(workingFile, workingDir, debug):
metaSim_infile = workingFile + ".fasta"
if os.path.exists(workingFile + "-454.fna"):
os.remove(workingFile + "-454.fna")
metaSim = runExtProg(metaSimDir + "./MetaSim", pdir=metaSimDir, length=9)
metaSim.set_param_at("cmd", 1)
metaSim.set_param_at("--454", 2)
metaSim.set_param_at("-f250", 3)
metaSim.set_param_at("-t25", 4)
metaSim.set_param_at("-r2000", 5)
metaSim.set_param_at("-c", 6)
metaSim.set_param_at("-d", 7)
metaSim.set_param_at(workingDir, 8)
metaSim.set_param_at(metaSim_infile, 9)
metaSim.run(debug)
def runSam2Fasta(workingFile, result_file_prefix, samfile_prefix, srp_read_prefix, error_free_model=True, debug=False):
reference_file = workingFile + ".cons"
srp_temp_file = workingFile + "_temp.fasta"
sam_outfile = workingFile + samfile_prefix + ".sam"
# sam2fasta = runExtProg(softwareDir + "./sam2fasta.py", length=3)
sam2fasta = runExtProg("./sam2fasta_mod.py", length=3)
sam2fasta.set_param_at(reference_file, 1)
sam2fasta.set_param_at(sam_outfile, 2)
sam2fasta.set_param_at(srp_temp_file, 3)
sam2fasta.run(debug)
shutil.copy(sam_outfile, result_file_prefix + samfile_prefix + ".sam")
shutil.copy(srp_temp_file, result_file_prefix + srp_read_prefix + samfile_prefix + ".fasta")
if error_free_model:
sam_outfile = workingFile + samfile_prefix + "_errFree.sam"
sam2fasta.set_param_at(sam_outfile, 2)
sam2fasta.run(debug)
shutil.copy(sam_outfile, result_file_prefix + samfile_prefix + "_errFree.sam")
shutil.copy(srp_temp_file, result_file_prefix + srp_read_prefix + samfile_prefix + "_errFree.fasta")