def execute_expression_analysis(self):
"""
Make analysis with counts data for mapping
:return:
"""
print("Expression analisys start...")
n = "consexpression"
out_merge_table = ""
if self._exp_dao._reference != "":
out_merge_table = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_table_count.txt"
self.execute_merge_table(self._count_table, out_merge_table)
else:
out_merge_table = self._merged_table_out
# 1 ------------------ edgeR -----------------
print("---- edgeR START! ------------")
out_expression = self._exp_dao._output + "/" + self._exp_dao._name
out_edger = out_expression + "_edger.csv"
self._edger = EdgeR(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_edger)
self._edger.run_edger()
# 2 ------------- BaySeq --------------------
print("---- baySeq START! ------------")
out_bayseq = out_expression + "_baySeq.csv"
self._bayseq = BaySeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_bayseq)
self._bayseq.run_bayseq()
# 3 ------------- DESeq --------------------
print("---- DESeq START! ------------")
out_deseq = out_expression + "_DESeq.csv"
self._deseq = DESeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_deseq)
self._deseq.run_deseq()
# 4 ------------- NOISeq --------------------
print("---- NOISeq START! ------------")
out_noiseq = out_expression + "_NOISeq.csv"
self._noiseq = Noiseq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_noiseq)
self._noiseq.run_noiseq()
# 5 ------------- EBSeq --------------------
print("---- EBSeq START! ------------")
out_ebseq = out_expression + "_EBSeq.csv"
self._ebseq = Ebseq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_ebseq)
self._ebseq.run_ebseq()
# 6 ------------- SAMSeq --------------------
print("---- SAMSeq START! ------------")
# out_samseq = out_expression + "_SAMSeq.csv"
# self._samseq = SamSeq(out_merge_table, self._exp_dao._group_name, self._exp_dao._replic, out_samseq)
# self._samseq.run_samseq()
# 7 ------------- limma-voom --------------------
print("---- limma START! ------------")
out_limmavoom = out_expression + "_limmavoom.csv"
self._limmavoom = LimmaVoom(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_limmavoom)
self._limmavoom.run_limmavoom()
def execute_expression_analysis(self):
"""
Make analysis with counts data for mapping
:return:
"""
print("Expression analisys start...")
n = "consexpression"
out_merge_table = ''
self.execute_merge_table(self._count_table, out_merge_table)
# 1 ------------------ edgeR -----------------
out_edger = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_edger.csv"
self._edger = EdgeR(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_edger)
self._edger.run_edger()
# 2 ------------- BaySeq --------------------
out_bayseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_baySeq.csv"
self._bayseq = BaySeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_bayseq)
self._bayseq.run_bayseq()
# 3 ------------- DESeq --------------------
out_deseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_DESeq.csv"
self._deseq = DESeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_deseq)
self._deseq.run_deseq()
# 4 ------------- NOISeq --------------------
out_noiseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_NOISeq.csv"
self._noiseq = Noiseq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_noiseq)
self._noiseq.run_noiseq()
# 5 ------------- EBSeq --------------------
out_ebseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_EBSeq.csv"
self._ebseq = Ebseq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_ebseq)
self._ebseq.run_ebseq()
# 6 ------------- SAMSeq --------------------
out_samseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_SAMSeq.csv"
self._samseq = SamSeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_samseq)
self._samseq.run_samseq()
# 7 ------------- limma-voom --------------------
out_limmavoom = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_limmavoom.csv"
self._limmavoom = LimmaVoom(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_limmavoom)
self._limmavoom.run_limmavoom()
class Experiment(object):
"""
Business object of Experiment
"""
def __init__(self):
print("-----------------------------------" +
"\n -- Welcome to consExpression -- " +
"\n---------------------------------\n")
self._exp_dao = None
self._reference = None
self._transcript = False
self._count = None
self._expression = None
self._mapp_bo = None
self.message = Message()
self._fastq = []
self._out_mapp = []
self._count_table = []
self._merged_table_out = None
self._edger = None
self._bayseq = None
self._deseq = None
self._noiseq = None
self._ebseq = None
self._samseq = None
self._limmavoom = None
def execute_expression_analysis(self):
"""
Make analysis with counts data for mapping
:return:
"""
print("Expression analisys start...")
n = "consexpression"
out_merge_table = ''
self.execute_merge_table(self._count_table, out_merge_table)
# 1 ------------------ edgeR -----------------
out_edger = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_edger.csv"
self._edger = EdgeR(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_edger)
self._edger.run_edger()
# 2 ------------- BaySeq --------------------
out_bayseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_baySeq.csv"
self._bayseq = BaySeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_bayseq)
self._bayseq.run_bayseq()
# 3 ------------- DESeq --------------------
out_deseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_DESeq.csv"
self._deseq = DESeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_deseq)
self._deseq.run_deseq()
# 4 ------------- NOISeq --------------------
out_noiseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_NOISeq.csv"
self._noiseq = Noiseq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_noiseq)
self._noiseq.run_noiseq()
# 5 ------------- EBSeq --------------------
out_ebseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_EBSeq.csv"
self._ebseq = Ebseq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_ebseq)
self._ebseq.run_ebseq()
# 6 ------------- SAMSeq --------------------
out_samseq = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_SAMSeq.csv"
self._samseq = SamSeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_samseq)
self._samseq.run_samseq()
# 7 ------------- limma-voom --------------------
out_limmavoom = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_limmavoom.csv"
self._limmavoom = LimmaVoom(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_limmavoom)
self._limmavoom.run_limmavoom()
class Experiment(object):
"""
Business object of Experiment
"""
_count: CountBo
def __init__(self):
self._exp_dao = None
self._reference = None
self._transcript = False
self._count = None
self._expression = None
self._mapp_bo = None
self.message = Message()
self._fastq = []
self._out_mapp = []
self._count_table = []
self._merged_table_out = None
self._edger = None
self._bayseq = None
self._deseq = None
self._noiseq = None
self._ebseq = None
self._samseq = None
self._limmavoom = None
def init_experiment(self, exp, file):
"""
Iniatialize experiment
:param exp:
:param file: config file
:return:
"""
assert isinstance(exp, ExperimentDao)
self._exp_dao = exp
self._exp_dao.read_configuration_file(file)
self._exp_dao._name = self.name_valid(self._exp_dao._name)
self.rep_valid(self._exp_dao._replic)
self.group_number_valid(self._exp_dao._group_number)
ref = self._exp_dao._reference
if self._exp_dao._reference == "":
print(
"You don't have a refserence genome... Expression analyse need a table count with mapping reads"
)
self._merged_table_out = input("Type absolute path to table count")
elif ref != "" and (self.extension_valid(ref, "fa")
or self.extension_valid(ref, "fasta")):
self._reference = self._exp_dao._reference # == ref
else:
self.message.message_3("REFERENCE FILE ")
exit(0)
self.directory_valid(self._exp_dao._read_directory, "reads")
for i in iter(self._exp_dao._group_directory):
reads = self._exp_dao._read_directory + "/" + str(i)
self.directory_valid(reads, "group")
# Get fastq reads
path_find = self._exp_dao._read_directory + "/" + i + "/"
self._fastq.append(self.get_reads_file(path_find))
if self._exp_dao._paired_end == True:
self.message.message_8(
"The sequence is paired-end. CONSEXPRESSION dont make paired-end analysis"
)
exit(0)
else:
self.message.message_8("The sequence is single-end")
def name_valid(self, name):
"""
Verify the name: if is empty change to default name
:param name: name of experiment
:return: boolean
"""
if len(name) == 0:
name = "consexpression"
self.message.message_7(
"Experiment name is empty! The name was changed to consexpression"
)
return name
def rep_valid(self, rep):
"""
Verify if number of replicates technical and biological is valid (>= 1).
basestring :param rep_t:
basestring :param rep_b:
void :return:
"""
ok = False
if rep >= 1:
self.message.message_1("replics")
else:
self.message.message_2(
"1 replic or more (technique or biological)")
self.message.message_3("number of replics in line 5 - 6")
exit()
def extension_valid(self, path, extension):
"""
Verify if the extension file is the expected
:param path:
:param extension:
:return: boolean
"""
var_ret = False
if str.endswith(path, extension):
var_ret = True
else:
var_ret = False
return var_ret
def directory_valid(self, path, type):
"""
Verify if path is a directory
:param path: path of file
:param type: file is reference genome, reads?
:return: void
"""
ok = os.path.isdir(path)
if ok:
self.message.message_1("directory " + type + ": " + path)
else:
self.message.message_2("a valid directory " + type + " path")
self.message.message_3(" the directory " + type + " path (line 9)")
exit()
def group_number_valid(self, group_n):
"""
Verify the number of groups. The minimal is one
int :param group_n:
void :return:
"""
assert isinstance(group_n, int)
if group_n >= 1:
self.message.message_1("group number")
else:
self.message.message_2("1 group or more.")
self.message.message_3("the number of gruoups in line 7")
exit()
def file_valid(self, path):
"""
Verify if path is a file
basestring :param path:
void :return:
"""
if os.path.isfile(path):
self.message.message_1(" file: " + path)
else:
self.message.message_2(" a valid reference file")
self.message.message_3(" the reference file path (line 7)")
exit()
def exceute_mapp_count(self):
"""
Execute Tophat and htseq-count
:return:
"""
ref = self._reference
thread = self._exp_dao._threads
sing = self._exp_dao._paired_end
n = self._exp_dao._name
path_find = []
for grp in iter(self._fastq):
for grp_file in iter(grp):
bar = 1 + grp_file.rfind('/')
out_mapp = grp_file[:bar] + n + "/" + grp_file[bar:]
dir = grp_file[:bar] + n
if os.path.isdir(dir):
pass
else:
os.mkdir(dir, 0o755)
out_mapp = out_mapp.replace('fastq', 'sam')
path_find.append(out_mapp)
mapp_vo = MappVo("TopHat", ref, grp_file, "", thread, out_mapp,
"", sing)
self._mapp_bo = MappBo(mapp_vo)
mapp_exe = self._mapp_bo.execute_mapp()
if mapp_exe == 0:
dot = out_mapp.rfind('.')
in_type = out_mapp[dot + 1:]
bar = 1 + out_mapp.rfind('/')
table_count = out_mapp[bar:dot]
table_count = out_mapp[:bar] + table_count + "_table_count.txt"
self._count_table.append(table_count)
in_count = out_mapp + "/accepted_hits.sam"
count_vo = CountVo(in_count,
self._exp_dao._annotation_file,
self._exp_dao._annotation_type, in_type,
self._exp_dao._count_mode, table_count)
self._count = CountBo(count_vo)
if self._count.execute_count() == 0:
self.message.message_8("Count Sucsessfull!!!")
else:
self.message.message_4(
"Error in counting mapped reads...")
else:
self.message.message_4(
"Task: Mapping don't run correctly.")
self._out_mapp.append(path_find)
def get_reads_file(self, dir):
"""
Get all fastq path of dir
:param dir: path to folder of fastq sample
:return: array of reads file path
"""
fastq_file = []
path = dir + "*.fastq" #serach
for file in glob.glob(path):
fastq_file.append(file)
if len(fastq_file) == 0:
self.message.message_7("*Not found files FASTQ in directorie " +
dir)
return fastq_file
def execute_expression_analysis(self):
"""
Make analysis with counts data for mapping
:return:
"""
print("Expression analisys start...")
n = "consexpression"
out_merge_table = ""
if self._exp_dao._reference != "":
out_merge_table = self._exp_dao._read_directory + "/" + self._exp_dao._name + "_table_count.txt"
self.execute_merge_table(self._count_table, out_merge_table)
else:
out_merge_table = self._merged_table_out
# 1 ------------------ edgeR -----------------
print("---- edgeR START! ------------")
out_expression = self._exp_dao._output + "/" + self._exp_dao._name
out_edger = out_expression + "_edger.csv"
self._edger = EdgeR(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_edger)
self._edger.run_edger()
# 2 ------------- BaySeq --------------------
print("---- baySeq START! ------------")
out_bayseq = out_expression + "_baySeq.csv"
self._bayseq = BaySeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_bayseq)
self._bayseq.run_bayseq()
# 3 ------------- DESeq --------------------
print("---- DESeq START! ------------")
out_deseq = out_expression + "_DESeq.csv"
self._deseq = DESeq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_deseq)
self._deseq.run_deseq()
# 4 ------------- NOISeq --------------------
print("---- NOISeq START! ------------")
out_noiseq = out_expression + "_NOISeq.csv"
self._noiseq = Noiseq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_noiseq)
self._noiseq.run_noiseq()
# 5 ------------- EBSeq --------------------
print("---- EBSeq START! ------------")
out_ebseq = out_expression + "_EBSeq.csv"
self._ebseq = Ebseq(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_ebseq)
self._ebseq.run_ebseq()
# 6 ------------- SAMSeq --------------------
print("---- SAMSeq START! ------------")
# out_samseq = out_expression + "_SAMSeq.csv"
# self._samseq = SamSeq(out_merge_table, self._exp_dao._group_name, self._exp_dao._replic, out_samseq)
# self._samseq.run_samseq()
# 7 ------------- limma-voom --------------------
print("---- limma START! ------------")
out_limmavoom = out_expression + "_limmavoom.csv"
self._limmavoom = LimmaVoom(out_merge_table, self._exp_dao._group_name,
self._exp_dao._replic, out_limmavoom)
self._limmavoom.run_limmavoom()
def execute_conseus(self, out):
gene_de = {}
read_bay = open(self._bayseq._output, 'r')
c_b = 0
for line in iter(read_bay):
if c_b > 0:
gene = line.split("\t")
v = self._bayseq.run_de(gene)
if gene[0] in gene_de:
aux = gene_de[gene[0]]
gene_de[gene[0]] = int(aux) + int(v)
else:
gene_de[gene[0]] = int(v)
c_b += 1
read_bay.close()
# ---- edger
read_edger = open(self._edger._output, 'r')
c_b = 0
for line in iter(read_edger):
if c_b > 0:
gene = line.split("\t")
v = self._edger.run_de(gene)
if gene[0] in gene_de:
aux = gene_de[gene[0]]
gene_de[gene[0]] = int(aux) + int(v)
else:
gene_de[gene[0]] = int(v)
c_b += 1
read_edger.close()
#--- deseq
read_deseq = open(self._deseq._output, 'r')
c_b = 0
for line in iter(read_deseq):
if c_b > 0:
gene = line.split("\t")
v = self._deseq.run_de(gene)
if gene[1] in gene_de:
aux = gene_de[gene[1]]
gene_de[gene[1]] = int(aux) + int(v)
else:
gene_de[gene[1]] = int(v)
c_b += 1
read_deseq.close()
# --- noiseq
read_noiseq = open(self._noiseq._output, 'r')
c_b = 0
for line in iter(read_noiseq):
if c_b > 0:
gene = line.split(",")
v = self._noiseq.run_de(gene)
if gene[0] in gene_de:
aux = gene_de[gene[0]]
gene_de[gene[0]] = int(aux) + int(v)
else:
gene_de[gene[0]] = int(v)
c_b += 1
read_noiseq.close()
# --- samseq
if self._samseq is None:
print("SAMSeq results not found")
else:
read_samseq = open(self._samseq._output, 'r')
c_b = 0
for line in iter(read_samseq):
if c_b > 0:
gene = line.split("\t")
v = self._samseq.run_de(gene)
if gene[1] in gene_de:
aux = gene_de[gene[1]]
gene_de[gene[1]] = int(aux) + int(v)
else:
gene_de[gene[1]] = int(v)
c_b += 1
read_samseq.close()
# --- limma
if self._exp_dao._replic >= 2:
read_limma = open(self._limmavoom._output, 'r')
c_b = 0
for line in iter(read_limma):
if c_b > 0:
gene = line.split("\t")
v = self._limmavoom.run_de(gene)
if gene[0] in gene_de:
aux = gene_de[gene[0]]
gene_de[gene[0]] = int(aux) + int(v)
else:
gene_de[gene[0]] = int(v)
c_b += 1
read_limma.close()
else:
print("limma require more than one replics")
# --- ebseq
read_ebseq = open(self._ebseq._output, 'r')
c_b = 0
for line in iter(read_ebseq):
if c_b > 0:
gene = line.split("\t")
v = self._ebseq.run_de(gene)
if gene[0] in gene_de:
aux = gene_de[gene[0]]
gene_de[gene[0]] = int(aux) + int(v)
else:
gene_de[gene[0]] = int(v)
c_b += 1
read_ebseq.close()
#--- write results
header = 'gene, indications'
out_cons = open(out, 'w')
out_cons.write(header)
names = gene_de.keys()
print(len(names))
for i in iter(names):
if (gene_de[i]) >= 4:
out_cons.write("\n" + i + "," + str(gene_de[i]))
def execute_merge_table(self, out_mapp_list, out_name):
"""
Make a merge table whit counts
:param out_mapp_list:
:param out_name:
:return:
"""
self._count.merge_table_count(out_mapp_list, out_name,
self._exp_dao._group_name)