Commit cec85510 authored by Penom Nom's avatar Penom Nom
Browse files

LAST COMMIT.

parent c15457db
......@@ -58,7 +58,7 @@ class SVDetection (NG6Workflow):
"output_file":"pindel.concat.out", "mean_insert":self.mean_insert,
"min_sup":self.min_sup, "indiv_list":indiv_list})
cnvnator = self.add_component("CnvNator", [input_bam, self.reference_genome, self.bin_size])
delly = self.add_component("Standardisation", [delly.output_file, "delly", "delly.bed", self.min_len, self.max_len, indiv_list])
pindel_tra = self.add_component("Standardisation", [pindel.output_file, "pindel_translocation", "pindel.bed", self.min_len, self.max_len, indiv_list])
pindel = self.add_component("Standardisation", [pindel.output_file, "pindel", "pindel.bed", self.min_len, self.max_len, indiv_list])
......@@ -66,9 +66,10 @@ class SVDetection (NG6Workflow):
cnvnator = self.add_component("Standardisation", [cnvnator.output_file, "cnvnator", "cnvnator.bed", self.min_len, self.max_len, indiv_list])
# #=====TEST PURPOSE===== translocation_file
# results = ["/home/yguarr/DataTest/delly.bed", "/home/yguarr/DataTest/breakdancer.bed", "/home/yguarr/DataTest/cnvnator.bed", "/home/yguarr/DataTest/pindel.bed"]
# translocations = ["/home/yguarr/DataTest/tra_breakdancer.bed"]
# #=====TEST PURPOSE=====
results=[delly.output_file, breakdancer.output_file, cnvnator.output_file, pindel.output_file]
translocations = [delly.translocation_file, breakdancer.translocation_file, cnvnator.translocation_file, pindel_tra.translocation_file]
arg_list = [results, self.overlap_percent, self.li_range, ["delly", "breakdancer","cnvnator","pindel"], options, translocations]
......
......@@ -130,7 +130,7 @@ class Analyzebed (Analysis):
svr = line.split()
svr_type = svr[4]
for column in svr[6].split(";"):
for column in svr[7].split(";"):
#get members
used_software.append("".join(column.split("-")[:-1]))
if svr_type not in venn_table_by_type: # create the dic
......
......@@ -170,9 +170,9 @@ def filter_out(sv, size_min, size_max):
#return True if we need to keep the SV
size = float(sv[5])
if size < int(size_min) or size > int(size_max):
return False
else:
return True
else:
return False
def main(SV_file_path, good_path, translocation_file, soft, tag, len_min, len_max, indiv_list, alt_names=[]):
"""
......
......@@ -26,6 +26,7 @@ class Pindel (Component):
self.add_input_file_list("input_bam", "One bam file by individual/condition", default=input_bam, file_format="bam", required=True)
self.add_input_file("reference_genome", "Animal ref file", default=reference_genome, file_format="fasta", required=True)
self.add_output_file("output_file", "Pindel concatenated output files [D/SI/TD/INV]", filename="pindel.concat.out")
self.add_output_file("tra_file", "Pindel translocations", filename="pindel.tra.out")
self.add_parameter("mean_insert", "mean insert size", type=int, default=mean_insert, required=True)
self.add_parameter("min_sup", "Minimum number of read supporting a SV (3) [Not available for cnvnator]", type=int, default=min_sup)
self.add_parameter_list("indiv_list", "String list of studied individuals name", default=indiv_list, type=str, required=True)
......@@ -59,4 +60,5 @@ class Pindel (Component):
" > $1", cmd_format='{EXE} {OUT} {ARG}')
chained_function = Pipeline(functions=[pindel,concatenate], separator="&&")
chained_function(arguments=[cfg_file_path, output_list], outputs=self.output_file)
#-k 4.7n -k3,3n
\ No newline at end of file
link = ShellFunction(self.get_exec_path("ln") + " -s $1 $2", cmd_format='{EXE} {IN} {OUT}')
link(inputs=output_pathway+"_INT_final", outputs=self.tra_file)
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