Commit 9897c125 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

No commit message

No commit message
parent 64d62eb6
...@@ -51,10 +51,8 @@ class MothurMakeContigs(Analysis): ...@@ -51,10 +51,8 @@ class MothurMakeContigs(Analysis):
else : self.reverse_primer = None else : self.reverse_primer = None
self.oligos_file = os.path.join(self.output_directory, 'oligos.oligos') self.oligos_file = os.path.join(self.output_directory, 'oligos.oligos')
else : self.oligos_file = None else : self.oligos_file = None
if maxambig : self.maxambig = maxambig self.maxambig = maxambig
else : self.maxambig = None self.maxlength = maxlength
if maxlength : self.maxlength = maxlength
else : self.maxlength = None
self.pdiffs = pdiffs self.pdiffs = pdiffs
self.processors = processors self.processors = processors
# define input files # define input files
...@@ -89,7 +87,7 @@ class MothurMakeContigs(Analysis): ...@@ -89,7 +87,7 @@ class MothurMakeContigs(Analysis):
self.options = '#make.contigs(file=stability.file,oligos=oligos.oligos,pdiffs='+str(self.pdiffs)+');' self.options = '#make.contigs(file=stability.file,oligos=oligos.oligos,pdiffs='+str(self.pdiffs)+');'
else: else:
self.options = '#make.contigs(file=stability.file);' self.options = '#make.contigs(file=stability.file);'
self.options += '#screen.seqs(fasta=FILE.fasta,group=FILE.groups,maxambig='+self.maxambig+',maxlength='+self.maxlength+');' self.options += '#screen.seqs(fasta=FILE.fasta,group=FILE.groups,maxambig='+str(self.maxambig)+',maxlength='+str(self.maxlength)+');'
def get_version(self): def get_version(self):
cmd = [self.get_exec_path("mothur"), "-version"] cmd = [self.get_exec_path("mothur"), "-version"]
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment