Commit 8dfecf58 authored by Maria Bernard's avatar Maria Bernard
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parent c2575e06
......@@ -32,7 +32,7 @@ from ng6.utils import Utils
class Ustacks (Analysis):
def define_parameters(self, indiv_dic, read1_files, min_cov=3, primary_mismatch=2, secondary_mismatch=4, max_locus=3, model_type="snp", alpha=0.05, bound_low=0, bound_high=1, bc_err_freq):
def define_parameters(self, indiv_dic, read1_files, min_cov=3, primary_mismatch=2, secondary_mismatch=4, max_locus=3, model_type="snp", alpha=0.05, bound_low=0, bound_high=1, bc_err_freq=0):
self.indiv_dic=indiv_dic
self.read1_files = InputFileList(read1_files, Formats.FASTQ)
self.min_cov = min_cov
......@@ -154,8 +154,7 @@ class Ustacks (Analysis):
def process(self):
for input in self.read1_files:
indiv = os.path.splitext(os.path.basename(input))[0] if os.path.splitext(os.path.basename(input))[1] != ".gz" else os.path.splitext(os.path.splitext(os.path.basename(input))[0])[0]
### comment on accede au param�tre de
indiv = os.path.splitext(os.path.basename(input))[0] if os.path.splitext(os.path.basename(input))[1] != ".gz" else os.path.splitext(os.path.splitext(os.path.basename(input))[0])[0]
id=self.indiv_dic[indiv]["id"]
format="fastq" if os.path.splitext(os.path.basename(input))[1] != ".gz" else gzfastq
ustacks = ShellFunction(self.get_exec_path("ustacks") + " -t " + format + " -f $1 -d -r -o " + self.output_directory + " -i " + id + \
......
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