Commit ebbee70f authored by Penom Nom's avatar Penom Nom
Browse files

maj

parent 8e0c637d
......@@ -33,8 +33,8 @@ class MothurClassifySeqs(Component):
self.processors = processors
#define input files
self.fasta_files = InputFileList(fasta_files, Formats.FASTA)
self.template_files = InputFileList(template_files, Formats.ANY)
self.database_taxonomy_files = InputFileList(taxonomy_files, Formats.ANY)
self.template_files = InputFile(template_files, Formats.ANY)
self.database_taxonomy_files = InputFile(taxonomy_files, Formats.ANY)
if names_files :self.names_files = InputFileList(names_files, Formats.MOTHUR_NAMES)
else: self.names_files = None
if groups_files : self.groups_files = InputFileList(groups_files, Formats.MOTHUR_GROUPS)
......@@ -49,20 +49,17 @@ class MothurClassifySeqs(Component):
def process(self):
print ">>>Process classify.seqs"
if self.names_files and not self.groups_files:
classifyseqs = ShellFunction(self.get_exec_path("mothur") + ' "#classify.seqs(fasta=$1,template=$2,taxonomy=$3,name=$4,cutoff='+str(self.cutoff)+\
',outputdir='+self.output_directory+'/,processors='+str(self.processors)+')" > $5', cmd_format='{EXE} {IN} {OUT}')
classifyseqs = MultiMap(classifyseqs, inputs=[self.fasta_files,self.template_files,self.database_taxonomy_files,self.names_files],\
outputs=[self.stdout,self.taxonomy_files,self.tax_summary_files])
classifyseqs = ShellFunction(self.get_exec_path("mothur") + ' "#classify.seqs(fasta=$1,template='+self.template_files+',taxonomy='+self.database_taxonomy_files+\
',name=$2,cutoff='+str(self.cutoff)+',outputdir='+self.output_directory+'/,processors='+str(self.processors)+')" > $3', cmd_format='{EXE} {IN} {OUT}')
classifyseqs = MultiMap(classifyseqs, inputs=[self.fasta_files,self.names_files],outputs=[self.stdout,self.taxonomy_files,self.tax_summary_files])
elif self.names_files and self.groups_files:
classifyseqs = ShellFunction(self.get_exec_path("mothur") + ' "#classify.seqs(fasta=$1,template=$2,taxonomy=$3,name=$4,group=$5,cutoff='+str(self.cutoff)+\
',outputdir='+self.output_directory+'/,processors='+str(self.processors)+')" > $6', cmd_format='{EXE} {IN} {OUT}')
classifyseqs = MultiMap(classifyseqs, inputs=[self.fasta_files,self.template_files,self.database_taxonomy_files,self.names_files,self.groups_files],\
outputs=[self.stdout,self.taxonomy_files,self.tax_summary_files])
classifyseqs = ShellFunction(self.get_exec_path("mothur") + ' "#classify.seqs(fasta=$1,template='+self.template_files+',taxonomy='+self.database_taxonomy_files+\
',name=$2,group=$3,cutoff='+str(self.cutoff)+',outputdir='+self.output_directory+'/,processors='+str(self.processors)+')" > $4', cmd_format='{EXE} {IN} {OUT}')
classifyseqs = MultiMap(classifyseqs, inputs=[self.fasta_files,self.names_files,self.groups_files],outputs=[self.stdout,self.taxonomy_files,self.tax_summary_files])
else:
classifyseqs = ShellFunction(self.get_exec_path("mothur") + ' "#classify.seqs(fasta=$1,template=$2,taxonomy=$3,cutoff='+str(self.cutoff)+\
',outputdir='+self.output_directory+'/,processors='+str(self.processors)+')" > $4', cmd_format='{EXE} {IN} {OUT}')
classifyseqs = MultiMap(classifyseqs, inputs=[self.fasta_files,self.template_files,self.database_taxonomy_files],\
outputs=[self.stdout,self.taxonomy_files,self.tax_summary_files])
classifyseqs = ShellFunction(self.get_exec_path("mothur") + ' "#classify.seqs(fasta=$1,template='+self.template_files+',taxonomy='+self.database_taxonomy_files+\
',cutoff='+str(self.cutoff)+',outputdir='+self.output_directory+'/,processors='+str(self.processors)+')" > $2', cmd_format='{EXE} {IN} {OUT}')
classifyseqs = MultiMap(classifyseqs, inputs=[self.fasta_files],outputs=[self.stdout,self.taxonomy_files,self.tax_summary_files])
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