def batch_for_batch():
os.chdir("/home/zerodel/Workspace/mouse/FullLengthMouse")
model_gtr = "rebuild_model.mdl"
model_nest = "rna_structure_full_mouse.mdl"
aln_path = "/home/zerodel/Workspace/mouse/mouse_8_species"
bf_maker_nest = BfH.HYPHYBatchFile(species_name="mouse", model_file=model_nest, bf_template_file="template_global")
bf_maker_gtr = BfH.HYPHYBatchFile(species_name="mouse", model_file=model_gtr, bf_template_file="template_global")
jobids = [file1.split(".")[0] for file1 in os.listdir(aln_path) if ".aln" == file1[-4:]]
for job_id in jobids:
aln_file_path_full = os.path.join(aln_path, job_id + ".aln")
input_file = os.path.join(os.curdir, job_id + ".input")
if not os.path.exists(input_file):
DH.aln2input(aln_file_path_full, input_file)
bfgtr = job_id + "gtr.bf"
bf_maker_gtr.write_batch_file(
dot_input=job_id + ".input",
dot_aln=aln_file_path_full,
hyphy_result_file=job_id + "gtr.result",
hyphy_batch_file=bfgtr,
)
bfnest = job_id + "nest.bf"
bf_maker_nest.write_batch_file(
dot_input=job_id + ".input",
dot_aln=aln_file_path_full,
hyphy_result_file=job_id + "nest.result",
hyphy_batch_file=bfnest,
)
def test_aln_to_no_gap_input(self):
try:
dh.check_sequence_matrix(["aaca", "aaa"])
except dh.sequenceNotSameLength:
pass
else:
self.fail("here should raise a exception!")
dh.aln2inputNogap("./tmp.aln","./tmp2.input")
def test_aln_to_no_gap_input(self):
try:
dh.check_sequence_matrix(["aaca", "aaa"])
except dh.sequenceNotSameLength:
pass
else:
self.fail("here should raise a exception!")
dh.aln2inputNogap("./tmp.aln", "./tmp2.input")
def make_bf_p2():
workpath = "d:\Workspace\Ecoli\P2"
os.chdir(workpath)
model_gtr = "rebuild_model.mdl"
model_nest = "rna_full_length_structure.mdl"
bf_maker_gtr = BfH.HYPHYBatchFile(species_name="ecoli",
model_file=model_gtr,
bf_template_file="templateNoGap")
bf_maker_nest = BfH.HYPHYBatchFile(species_name="ecoli",
model_file=model_nest,
bf_template_file="templateNoGap")
bf_maker_gtr.set_tree_from_outside(SS.ecoli())
bf_maker_nest.set_tree_from_outside(SS.ecoli())
aln_file_folder = "d:\Workspace\Ecoli\ecoli_10_species"
aln_files = [file_single for file_single in os.listdir(aln_file_folder) if ".aln" == os.path.splitext(file_single)[-1]]
for single_aln in aln_files:
aln_full_path = os.path.join(aln_file_folder, single_aln)
genes, lengths = DH.aln_info(aln_full_path)
gene_full_length = lengths[0]
jobid = single_aln.split(".")[0]
input_file_name = "%s.input" % jobid
DH.aln2input(aln_full_path, input_file_name)
if gene_full_length < 52:
print "%s too short ---" % single_aln
continue
bf_maker_gtr.set_partition(51, gene_full_length)
bf_maker_nest.set_partition(51, gene_full_length)
bf_maker_gtr.write_batch_file(dot_input=input_file_name,
dot_aln="",
hyphy_batch_file="%sp2gtr.bf" % jobid,
hyphy_result_file="%sp2gtr.result" % jobid)
bf_maker_nest.write_batch_file(dot_input=input_file_name,
dot_aln="",
hyphy_batch_file="%sp2nest.bf" % jobid,
hyphy_result_file="%sp2nest.result" % jobid)
def write_batch_file(self, dot_input, dot_aln, hyphy_batch_file="", hyphy_result_file=""):
""" write a .bf file for a alignment"""
gene_id = os.path.basename(dot_input).split(os.path.extsep)[0]
path_main = os.path.splitext(dot_input)[0]
if "" == hyphy_batch_file:
hyphy_batch_file = path_main + ".bf"
if "" == hyphy_result_file:
hyphy_result_file = path_main + ".result"
if "" == self.batch_content:
raise BFError
# replace begins here
batch_content, num_hits = re.subn(self.f_input, dot_input, self.batch_content)
self._error_no_hit(num_hits)
# partition is optional
if (0, 0) == self.partition:
if self.f_partition in batch_content:
batch_content, num_hits = re.subn(self.f_partition, "", batch_content)
self._error_no_hit(num_hits)
else:
batch_content, num_hits = re.subn(self.f_partition, "%d-%d" % self.partition, batch_content)
self._error_no_hit(num_hits)
batch_content, num_hits = re.subn(self.f_mdl, self.mdl_file, batch_content)
self._error_no_hit(num_hits)
# only support 1 matrix now :2014-5-26
batch_content, num_hits = re.subn(self.f_matrix_name, self.matrix_name[0], batch_content)
self._error_no_hit(num_hits)
if self.use_given_tree:
tree_newick_string = self.tree_definition_external
else:
genes_share_aln = pHdata.aln_reader(dot_aln)
tree_newick_string = self.build_tree(genes_share_aln)
batch_content, num_hits = re.subn(self.f_tree, tree_newick_string, batch_content)
self._error_no_hit(num_hits)
batch_content, num_hits = re.subn(self.f_output, hyphy_result_file, batch_content)
self._error_no_hit(num_hits)
self.check_whether_incomplete(batch_content)
with open(name=hyphy_batch_file, mode="w") as bf_writer:
bf_writer.write(batch_content)
def check_gene_order_in_alignments(path_to_alignments):
"""
判断path_to_alignment 里面所有的.aln 文件里物种名是否都是一样的.
:param path_to_alignments:
:return:
"""
# get file-names
import os
import os.path
current_dir = os.path.abspath(os.curdir)
os.chdir(path_to_alignments)
aln_files = [single_file for single_file in os.listdir(path_to_alignments)
if ".aln" == os.path.splitext(single_file)[-1]]
try:
import pyHYPHY.DataHYPHY as dh
except ImportError:
print "error in importing pyHYPHY module"
return
aln_genes_calibration = dh.aln_info(aln_files[0])[0]
gene_un_match = 0
for aln_entry in aln_files:
if not aln_genes_calibration == dh.aln_info(aln_entry)[0]:
print aln_entry, ":---- ", str(dh.aln_info(aln_entry)[0]), "\n"
gene_un_match += 1
print "whole number of unmatch file is %d \n and pattern is :\n %s \n" % (gene_un_match, aln_genes_calibration)
os.chdir(current_dir)
if 0 == gene_un_match:
return aln_genes_calibration
else:
raise AlignmentNotSame
def batch_for_batch():
os.chdir("/home/zerodel/Workspace/mouse/FullLengthMouse")
model_gtr = "rebuild_model.mdl"
model_nest = "rna_structure_full_mouse.mdl"
aln_path = "/home/zerodel/Workspace/mouse/mouse_8_species"
bf_maker_nest = BfH.HYPHYBatchFile(species_name="mouse",
model_file=model_nest,
bf_template_file="template_global")
bf_maker_gtr = BfH.HYPHYBatchFile(species_name="mouse",
model_file=model_gtr,
bf_template_file="template_global")
jobids = [
file1.split(".")[0] for file1 in os.listdir(aln_path)
if ".aln" == file1[-4:]
]
for job_id in jobids:
aln_file_path_full = os.path.join(aln_path, job_id + ".aln")
input_file = os.path.join(os.curdir, job_id + ".input")
if not os.path.exists(input_file):
DH.aln2input(aln_file_path_full, input_file)
bfgtr = job_id + "gtr.bf"
bf_maker_gtr.write_batch_file(dot_input=job_id + ".input",
dot_aln=aln_file_path_full,
hyphy_result_file=job_id + "gtr.result",
hyphy_batch_file=bfgtr)
bfnest = job_id + "nest.bf"
bf_maker_nest.write_batch_file(dot_input=job_id + ".input",
dot_aln=aln_file_path_full,
hyphy_result_file=job_id +
"nest.result",
hyphy_batch_file=bfnest)
def check_aln_full_species(folder_alns):
all_alns = [single_file for single_file in os.listdir(folder_alns) if single_file[-4:] == ".aln"]
aln_gene_num = []
for single_file in all_alns:
full_aln_path = os.path.join(folder_alns, single_file)
genes, gene_lengths = dh.aln_info(full_aln_path)
aln_gene_num.append(len(genes))
max_num = max(aln_gene_num)
aln_full_gene = []
for indexI, aln in enumerate(all_alns):
if aln_gene_num[indexI] == max_num:
aln_full_gene.append(all_alns[indexI])
return aln_full_gene
def check_aln_full_species(folder_alns):
all_alns = [
single_file for single_file in os.listdir(folder_alns)
if single_file[-4:] == ".aln"
]
aln_gene_num = []
for single_file in all_alns:
full_aln_path = os.path.join(folder_alns, single_file)
genes, gene_lengths = dh.aln_info(full_aln_path)
aln_gene_num.append(len(genes))
max_num = max(aln_gene_num)
aln_full_gene = []
for indexI, aln in enumerate(all_alns):
if aln_gene_num[indexI] == max_num:
aln_full_gene.append(all_alns[indexI])
return aln_full_gene
def check_aln_files():
"""
check which .aln file contains gene of all 10 species
:return:
"""
folder_alns = "/media/zerodel/Home/Work/custom/ecoli_aln"
all_alns = [single_file for single_file in os.listdir(folder_alns) if single_file[-4:] == ".aln"]
aln_gene_num = []
for single_file in all_alns:
full_aln_path = os.path.join(folder_alns, single_file)
genes, gene_lengths = DataHyPHY.aln_info(full_aln_path)
aln_gene_num.append(len(genes))
max_num = max(aln_gene_num)
aln_full_gene = []
for indexI, aln in enumerate(all_alns):
if aln_gene_num[indexI] == max(aln_gene_num):
aln_full_gene.append(all_alns[indexI])
print "fulllength has", len(aln_full_gene), "with ", str(max_num), "genes"
def check_aln_files():
"""
check which .aln file contains gene of all 10 species
:return:
"""
folder_alns = "/media/zerodel/Home/Work/custom/ecoli_aln"
all_alns = [
single_file for single_file in os.listdir(folder_alns)
if single_file[-4:] == ".aln"
]
aln_gene_num = []
for single_file in all_alns:
full_aln_path = os.path.join(folder_alns, single_file)
genes, gene_lengths = DataHyPHY.aln_info(full_aln_path)
aln_gene_num.append(len(genes))
max_num = max(aln_gene_num)
aln_full_gene = []
for indexI, aln in enumerate(all_alns):
if aln_gene_num[indexI] == max(aln_gene_num):
aln_full_gene.append(all_alns[indexI])
print "fulllength has", len(aln_full_gene), "with ", str(max_num), "genes"
def test_something(self):
raw_sequence = "aca----gt"
gap_removed = "aca"
self.assertEqual(gap_removed, dh.remove_gaps(raw_sequence))
def test_remove_gap_matrix(self):
raw_matrix = ["aaa--a", "bbbcac"]
fileterd_matrix = ["aaa", "bbb"]
self.assertEqual(fileterd_matrix, dh.remove_gaps_matrix(raw_matrix))
current_dir = os.path.abspath(os.curdir)
os.chdir(path_aln_file)
species_list = check_gene_order_in_alignments(path_aln_file)
inputfile_header = [">%s" % species_name for species_name in species_list]
matrix_sequence = ["" for species_name in species_list]
aln_files = [single_file for single_file in os.listdir(path_aln_file)
if ".aln" == os.path.splitext(single_file)[-1]]
for single_aln_file in aln_files:
# single file operation
# rejection : 1. length not enough 2 two many gaps
try:
<<<<<<< HEAD
matrix_sequence = paste_matrix(matrix_sequence,DH.remove_gaps_matrix(extract_TIR_single_file(single_aln_file, length_of_TIR, start_point)))
=======
if remove_gap:
gene_seq_matrix_addition = DH.remove_gaps_matrix(extract_TIR_single_file(single_aln_file, length_of_TIR, start_point))
else:
gene_seq_matrix_addition = extract_TIR_single_file(single_aln_file, length_of_TIR, start_point)
matrix_sequence = paste_matrix(matrix_sequence, gene_seq_matrix_addition)
>>>>>>> f0acd743d1106c96b88083b2df2cb3526b388aec
except SequenceTooShort:
print "Too short in %s" % single_aln_file
continue
except DimNotSame:
print "Error of Dimisions %s" % single_aln_file
def aln_folder_traversal(folder_name):
""" """
built_in_gy94mdl = "/usr/lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl"
gy94bf = bfHYPHY.HYPHYBatchFile(species_name="ecoli",
model_file=built_in_gy94mdl,
bf_template_file="partition.bf")
own_model = "nest_gy.mdl"
nested_model = bfHYPHY.HYPHYBatchFile(species_name="ecoli",
model_file=own_model,
bf_template_file="partition.bf")
nt_nest_model = "nt_nest_gy.mdl"
bf_nt_nest = bfHYPHY.HYPHYBatchFile(species_name="ecoli",
model_file=nt_nest_model,
bf_template_file="partition.bf")
gu_model = "myCodonMatrix.def"
gu_bf = bfHYPHY.HYPHYBatchFile(species_name="ecoli",
model_file=gu_model,
bf_template_file="synAlphaWPsiModelP.bf")
pwd = os.path.abspath(folder_name)
os.chdir(folder_name)
aln_files = [file1
for file1 in os.listdir(pwd)
if "aln" == file1.split(".")[-1]]
for index, aln_name in enumerate(aln_files):
# write batch file for each aln
gene_id = aln_name.split(".")[0]
genes, gene_len = dataHYPHY.aln_info(aln_name)
len_gene = max(gene_len)
gy94bf1 = "%sgy94.bf" % gene_id
input_filename = "%s.input" % gene_id
# input file here
dataHYPHY.aln2input(dot_aln_file=aln_name, hyphy_input_file=input_filename)
# gy model , full length
gy94bf.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_batch_file=gy94bf1,
hyphy_result_file="gy94%s_%s.result" % (gene_id, ""))
# gy model , part 1
gy94p1_name = "%sgy94p1.bf" % gene_id
gy94bf.set_partition(0, 60)
gy94bf.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_batch_file=gy94p1_name,
hyphy_result_file="gy94p1%s_%s.result" % (gene_id, ""))
# gy model , part 2
gy94p2_name = "%sgy94p2.bf" % gene_id
gy94bf.set_partition(60, len_gene)
gy94bf.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_batch_file=gy94p2_name,
hyphy_result_file="gy94p2%s_%s.result" % (gene_id, ""))
# nested model , full length
nested_model.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="nest_gy%s.result" % gene_id,
hyphy_batch_file="%snest_gy.bf" % gene_id)
# nested model , part 1
nested_model.set_partition(0, 60)
nested_model.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="nest_gy%s_p1.result" % gene_id,
hyphy_batch_file="%snest_gyp1.bf" % gene_id)
# nested model , part 2
nested_model.set_partition(60, len_gene)
nested_model.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="nest_gy%s_p2.result" % gene_id,
hyphy_batch_file="%snest_gyp2.bf" % gene_id)
# nt nested ,full
bf_nt_nest.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="%snt_nest.result" % gene_id,
hyphy_batch_file="%snt_nest.bf" % gene_id)
# nt nested , part1
bf_nt_nest.set_partition(0, 60)
bf_nt_nest.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="%snt_nest_p1.result" % gene_id,
hyphy_batch_file="%snt_nest_p1.bf" % gene_id)
# nt nested , part2
bf_nt_nest.set_partition(60, len_gene)
bf_nt_nest.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="%snt_nest_p2.result" % gene_id,
hyphy_batch_file="%snt_nest_p2.bf" % gene_id)
# gu model . full length
gu_bf.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="%sgu.result" % gene_id,
hyphy_batch_file="%sgu.bf" % gene_id)
gu_bf.set_partition(0, 60)
gu_bf.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="%sgup1.result" % gene_id,
hyphy_batch_file="%sgup1.bf" % gene_id)
gu_bf.set_partition(60 ,len_gene)
gu_bf.write_batch_file(dot_aln=aln_name,
dot_input=input_filename,
hyphy_result_file="%sgup2.result" % gene_id,
hyphy_batch_file="%sgup2.bf" % gene_id)
def main():
# main part
aln_files_folder = "d:/Workspace/Ecoli/ecoli_10_species"
#aln_files_folder = "d:/Workspace/Ecoli/test"
target_path = "d:/Workspace/Ecoli/NoGapP1"
aln_files = [single_file for single_file in os.listdir(aln_files_folder)
if ".aln" == os.path.splitext(single_file)[-1]]
model_gtr = "rebuild_model.mdl"
model_nest = "rna_full_length_structure.mdl"
job_ids = []
seq_length = []
for aln in aln_files:
aln_path_full = os.path.join(aln_files_folder, aln)
gene_in_aln, length_in_aln = dh.aln_info(aln_path_full)
seq_length.append(length_in_aln[0])
job_id = aln.split(".")[0]
if 10 == len(gene_in_aln): # only those gene shared in 10 species
job_ids.append(job_id)
input_file_path_full = os.path.join(target_path, job_id + ".input")
shutil.copyfile(aln_path_full, os.path.join(target_path, aln))
# write input file
dh.aln2inputNogap(aln_path_full, input_file_path_full)
# make bf file for full length no gap gtr and empirical model
os.chdir(target_path)
bf_maker_nest = BfH.HYPHYBatchFile(species_name="ecoli",
model_file=model_nest,
bf_template_file="templateNoGap")
bf_maker_gtr = BfH.HYPHYBatchFile(species_name="ecoli",
model_file=model_gtr,
bf_template_file="templateNoGap")
for job_id in job_ids:
# aln_path_full = os.path.join(aln_files_folder,aln)
# input_file_path_full = os.path.join(target_path, job_id + ".input")
# shutil.copyfile(aln_path_full, os.path.join(target_path,aln))
# # write input file
# dh.aln2inputNogap(aln_path_full, input_file_path_full)
# make bf file for full length no gap gtr and empirical model
bfgtr = job_id + "gtr.bf"
bf_maker_gtr.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id + "gtr.result",
hyphy_batch_file=bfgtr)
bfnest = job_id + "nest.bf"
bf_maker_nest.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id + "nest.result",
hyphy_batch_file=bfnest)
bf_maker_gtr.set_partition(0, 51)
bf_maker_nest.set_partition(0, 51)
for job_id in job_ids:
bfgtr = job_id + "gtrp1.bf"
bf_maker_gtr.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id + "gtrp1.result",
hyphy_batch_file=bfgtr)
bfnest = job_id + "nestp1.bf"
bf_maker_nest.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id + "nestp1.result",
hyphy_batch_file=bfnest)
for indexI, job_id in enumerate(job_ids):
bf_maker_gtr.set_partition(51, seq_length[indexI])
bf_maker_nest.set_partition(51, seq_length[indexI])
bfgtr = job_id + "gtrp2.bf"
bf_maker_gtr.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id + "gtrp2.result",
hyphy_batch_file=bfgtr)
bfnest = job_id + "nestp2.bf"
bf_maker_nest.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id + "nestp2.result",
hyphy_batch_file=bfnest)
def test_remove_gap_matrix(self):
raw_matrix = ["aaa--a", "bbbcac"]
fileterd_matrix = ["aaa", "bbb"]
self.assertEqual(fileterd_matrix, dh.remove_gaps_matrix(raw_matrix))
def main():
# main part
aln_files_folder = "d:/Workspace/Ecoli/ecoli_10_species"
#aln_files_folder = "d:/Workspace/Ecoli/test"
target_path = "d:/Workspace/Ecoli/NoGapP1"
aln_files = [
single_file for single_file in os.listdir(aln_files_folder)
if ".aln" == os.path.splitext(single_file)[-1]
]
model_gtr = "rebuild_model.mdl"
model_nest = "rna_full_length_structure.mdl"
job_ids = []
seq_length = []
for aln in aln_files:
aln_path_full = os.path.join(aln_files_folder, aln)
gene_in_aln, length_in_aln = dh.aln_info(aln_path_full)
seq_length.append(length_in_aln[0])
job_id = aln.split(".")[0]
if 10 == len(gene_in_aln): # only those gene shared in 10 species
job_ids.append(job_id)
input_file_path_full = os.path.join(target_path, job_id + ".input")
shutil.copyfile(aln_path_full, os.path.join(target_path, aln))
# write input file
dh.aln2inputNogap(aln_path_full, input_file_path_full)
# make bf file for full length no gap gtr and empirical model
os.chdir(target_path)
bf_maker_nest = BfH.HYPHYBatchFile(species_name="ecoli",
model_file=model_nest,
bf_template_file="templateNoGap")
bf_maker_gtr = BfH.HYPHYBatchFile(species_name="ecoli",
model_file=model_gtr,
bf_template_file="templateNoGap")
for job_id in job_ids:
# aln_path_full = os.path.join(aln_files_folder,aln)
# input_file_path_full = os.path.join(target_path, job_id + ".input")
# shutil.copyfile(aln_path_full, os.path.join(target_path,aln))
# # write input file
# dh.aln2inputNogap(aln_path_full, input_file_path_full)
# make bf file for full length no gap gtr and empirical model
bfgtr = job_id + "gtr.bf"
bf_maker_gtr.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id + "gtr.result",
hyphy_batch_file=bfgtr)
bfnest = job_id + "nest.bf"
bf_maker_nest.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id +
"nest.result",
hyphy_batch_file=bfnest)
bf_maker_gtr.set_partition(0, 51)
bf_maker_nest.set_partition(0, 51)
for job_id in job_ids:
bfgtr = job_id + "gtrp1.bf"
bf_maker_gtr.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id +
"gtrp1.result",
hyphy_batch_file=bfgtr)
bfnest = job_id + "nestp1.bf"
bf_maker_nest.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id +
"nestp1.result",
hyphy_batch_file=bfnest)
for indexI, job_id in enumerate(job_ids):
bf_maker_gtr.set_partition(51, seq_length[indexI])
bf_maker_nest.set_partition(51, seq_length[indexI])
bfgtr = job_id + "gtrp2.bf"
bf_maker_gtr.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id +
"gtrp2.result",
hyphy_batch_file=bfgtr)
bfnest = job_id + "nestp2.bf"
bf_maker_nest.write_batch_file(dot_input=job_id + ".input",
dot_aln=job_id + ".aln",
hyphy_result_file=job_id +
"nestp2.result",
hyphy_batch_file=bfnest)
def test_something(self):
raw_sequence = "aca----gt"
gap_removed = "aca"
self.assertEqual(gap_removed, dh.remove_gaps(raw_sequence))
def write_batch_file(self,
dot_input,
dot_aln,
hyphy_batch_file="",
hyphy_result_file=""):
""" write a .bf file for a alignment"""
gene_id = os.path.basename(dot_input).split(os.path.extsep)[0]
path_main = os.path.splitext(dot_input)[0]
if "" == hyphy_batch_file:
hyphy_batch_file = path_main + ".bf"
if "" == hyphy_result_file:
hyphy_result_file = path_main + ".result"
if "" == self.batch_content:
raise BFError
# replace begins here
batch_content, num_hits = re.subn(self.f_input, dot_input,
self.batch_content)
self._error_no_hit(num_hits)
# partition is optional
if (0, 0) == self.partition:
if self.f_partition in batch_content:
batch_content, num_hits = re.subn(self.f_partition, "",
batch_content)
self._error_no_hit(num_hits)
else:
batch_content, num_hits = re.subn(self.f_partition,
"%d-%d" % self.partition,
batch_content)
self._error_no_hit(num_hits)
batch_content, num_hits = re.subn(self.f_mdl, self.mdl_file,
batch_content)
self._error_no_hit(num_hits)
# only support 1 matrix now :2014-5-26
batch_content, num_hits = re.subn(self.f_matrix_name,
self.matrix_name[0], batch_content)
self._error_no_hit(num_hits)
if self.use_given_tree:
tree_newick_string = self.tree_definition_external
else:
genes_share_aln = pHdata.aln_reader(dot_aln)
tree_newick_string = self.build_tree(genes_share_aln)
batch_content, num_hits = re.subn(self.f_tree, tree_newick_string,
batch_content)
self._error_no_hit(num_hits)
batch_content, num_hits = re.subn(self.f_output, hyphy_result_file,
batch_content)
self._error_no_hit(num_hits)
self.check_whether_incomplete(batch_content)
with open(name=hyphy_batch_file, mode="w") as bf_writer:
bf_writer.write(batch_content)
