def make_bf_TIR():
workpath = "d:\Workspace\Ecoli\combinedP1"
os.chdir(workpath)
model_gtr = "rebuild_model.mdl"
model_nest = "rna_full_length_structure.mdl"
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")
bf_maker_gtr.set_tree_from_outside(SS.ecoli())
bf_maker_nest.set_tree_from_outside(SS.ecoli())
for window_width_offset in range(15):
length_window = 30 + 5*window_width_offset
aln_files = "d:\Workspace\Ecoli\ecoli_10_species"
extracted_input_file = workpath + "\TIR" + str(length_window) + ".input"
gene_conjunction(aln_files, extracted_input_file, length_window)
bf_maker_gtr.write_batch_file(dot_input="TIR%d.input" % length_window,
dot_aln="",
hyphy_batch_file="TIR%dgtr.bf" % length_window,
hyphy_result_file="TIR%dgtr.result" % length_window)
bf_maker_nest.write_batch_file(dot_input="TIR%d.input" % length_window,
dot_aln="",
hyphy_batch_file="TIR%dnest.bf" % length_window,
hyphy_result_file="TIR%dnest.result" % length_window)
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 test_bf():
bf1 = bf.HYPHYBatchFile(species_name="ecoli",
model_file="../rebuild_model.mdl",
bf_template_file="../pyHYPHY/templateNoGap")
bf1.use_given_tree = True
bf1.tree_definition_external = "(g1,g2)"
bf1.write_batch_file("./tmp2.input", "./tmp.aln", "xxx.bf", "xxx.result")
def sliding_window():
workpath = "d:\Workspace\Ecoli\slidingWindow"
os.chdir(workpath)
model_gtr = "rebuild_model.mdl"
model_nest = "rna_full_length_structure.mdl"
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")
bf_maker_gtr.set_tree_from_outside(SS.ecoli())
bf_maker_nest.set_tree_from_outside(SS.ecoli())
step_num = 15
step_width_step = 5
window_width_min = 30
site_start_point = 0
site_shift_step = 5
for window_start_offset in range(step_num):
for window_width_offset in range(step_num):
start_site = site_shift_step*window_start_offset + site_start_point
length_window = step_width_step*window_width_offset + window_width_min
aln_files = "d:\Workspace\Ecoli\ecoli_10_species"
# extracted_input_file = workpath + "\TIR" + str(length_window) + ".input"
job_description = "w%ds%d" % (length_window, start_site)
extracted_input_file = "%s\\TIR%s.input" % (workpath, job_description)
print extracted_input_file
gene_conjunction(aln_files, extracted_input_file, length_window, start_site)
bf_maker_gtr.write_batch_file(dot_input="TIR%s.input" % job_description,
dot_aln="",
hyphy_batch_file="TIR%sgtr.bf" % job_description,
hyphy_result_file="TIR%sgtr.result" % job_description)
bf_maker_nest.write_batch_file(dot_input="TIR%s.input" % job_description,
dot_aln="",
hyphy_batch_file="TIR%snest.bf" % job_description,
hyphy_result_file="TIR%snest.result" % job_description)
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 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 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 sliding_window():
"""perform a sliding window analysis over sequence alignment
"""
workpath = "/Users/zerodel/WorkSpace/test/test_slidingWindow"
# important here, has changed path.
os.chdir(workpath)
model_gtr = "rebuild_model.mdl"
model_nest = "rna_full_length_structure.mdl"
aln_files = "/Users/zerodel/WorkSpace/ecoli_aln"
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")
bf_maker_gtr.set_tree_from_outside(SS.ecoli())
bf_maker_nest.set_tree_from_outside(SS.ecoli())
step_num = 21
step_width_step = 15
window_width_min = 30
site_start_point = 0
site_shift_step = 15
window_axis = [0,2]
start_axis = range(step_num)
for window_width_offset in window_axis:
for window_start_offset in start_axis:
start_site = site_shift_step*window_start_offset + site_start_point
length_window = step_width_step*window_width_offset + window_width_min
# extracted_input_file = workpath + "\TIR" + str(length_window) + ".input"
job_description = "w%ds%d" % (length_window, start_site)
extracted_input_file = "TIR%s.input" % job_description
extracted_input_no_gap = "TIR%sN.input" % job_description
gene_conjunction(aln_files, os.path.join(workpath, extracted_input_file), length_window, start_site)
gene_conjunction(aln_files, os.path.join(workpath, extracted_input_no_gap), length_window, start_site, False)
bf_maker_gtr.write_batch_file(dot_input=extracted_input_file,
dot_aln="",
hyphy_batch_file="TIR%sgtr.bf" % job_description,
hyphy_result_file="TIR%sgtr.result" % job_description)
bf_maker_nest.write_batch_file(dot_input=extracted_input_file,
dot_aln="",
hyphy_batch_file="TIR%snest.bf" % job_description,
hyphy_result_file="TIR%snest.result" % job_description)
# no gap
bf_maker_gtr.write_batch_file(dot_input=extracted_input_no_gap,
dot_aln="",
hyphy_batch_file="TIR%sgtrN.bf" % job_description,
hyphy_result_file="TIR%sgtrN.result" % job_description)
bf_maker_nest.write_batch_file(dot_input=extracted_input_no_gap,
dot_aln="",
hyphy_batch_file="TIR%snestN.bf" % job_description,
hyphy_result_file="TIR%snestN.result" % job_description)