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Commit 9b606774 authored by Penom Nom's avatar Penom Nom
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fix bug label in otuanalysis component

parent a0cdc5c3
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workflows/components/mothurotuanalysis.py
View file @ 9b606774
......@@ -21,8 +21,8 @@ def get_taxonomy_to_Krona(exec_krona,output_directory,*files):
#case of 454
start = "an."
end = ".cons"
substrings = map(lambda string : re.search('%s(.*)%s' % (start, end), string).group(1),taxonomy_files)
result = dict(zip(substrings,taxonomy_files))
substrings_labels = map(lambda string : re.search('%s(.*)%s' % (start, end), string).group(1),taxonomy_files)
result = dict(zip(substrings_labels,taxonomy_files))
taxonomy_outputs = []
for label, tax_file in result.items():
source = tax_file
......@@ -117,12 +117,7 @@ class MothurOTUAnalysis(Analysis):
:param freq :
:type freq : int
"""
#define parameters
self.calc = calc
self.tree_calc = tree_calc
self.label = label
self.tree_label = tree_label
self.freq = freq
#define input files
self.an_list_files = InputFileList(an_list_files)
self.taxonomy_files = InputFileList(taxonomy_files, Formats.MOTHUR_TAXONOMY)
......@@ -134,9 +129,16 @@ class MothurOTUAnalysis(Analysis):
else : self.groups_files = None
if count_table_files : self.count_table_files = InputFileList(count_table_files, Formats.MOTHUR_COUNT_TABLE)
else : self.count_table_files = None
labels = self.label.split('-')
#define parameters
self.calc = calc
self.tree_calc = tree_calc
self.tree_label = tree_label
self.freq = freq
labels = label.split('-')
user_labels = [lines.split('\t')[0] for lines in open(self.an_list_files[0]).readlines()]
good_label = list(set(user_labels).intersection(set(labels)))
good_labels = list(set(user_labels).intersection(set(labels)))
self.label = good_labels
#define makeshared output files
self.shared_files = OutputFileList(self.get_outputs('{basename_woext}.shared', self.an_list_files))
self.makeshared_stdout = OutputFileList(self.get_outputs('{basename_woext}.makeshared.stdout', self.an_list_files))
......@@ -147,7 +149,7 @@ class MothurOTUAnalysis(Analysis):
self.rarefaction_single_files = OutputFileList(self.get_outputs('{basename_woext}.groups.rarefaction', self.shared_files))
self.rarefactionsingle_stdout = OutputFileList(self.get_outputs('{basename_woext}.rarefactionsingle.stdout', self.shared_files))
#define treeshared output files
# list_tree_files = [os.path.splitext(self.shared_files[0])[0]+"."+tree_calc+"."+label+".tre" for label in good_label]
# list_tree_files = [os.path.splitext(self.shared_files[0])[0]+"."+tree_calc+"."+label+".tre" for label in self.label]
# self.tree_files = OutputFileList(self.get_outputs('{basename}', list_tree_files))
# self.treeshared_stdout = OutputFileList(self.get_outputs('{basename_woext}.treeshared.stdout', self.shared_files))
#define subsample output files
......@@ -159,23 +161,21 @@ class MothurOTUAnalysis(Analysis):
self.subsample_count_files = OutputFileList(self.get_outputs('{basename_woext}.subsample.count_table', self.count_table_files), Formats.MOTHUR_COUNT_TABLE)
self.subsample_stdout = OutputFileList(self.get_outputs('{basename_woext}.subsample.stdout', self.count_table_files))
#define classifyotu output files
self.cons_taxonomy_files = OutputFileList([os.path.join(self.output_directory,l+".taxonomy") for l in good_label],Formats.MOTHUR_TAXONOMY)
#self.cons_tax_taxonomy_files = OutputFileList(self.get_outputs('{basename_woext}.'+str(self.label.split('-')[0])+'.cons.tax.summary', self.an_list_files))
self.cons_taxonomy_files = OutputFileList([os.path.join(self.output_directory,l+".taxonomy") for l in self.label],Formats.MOTHUR_TAXONOMY)
self.classifyotu_stdout = OutputFileList(self.get_outputs('{basename_woext}.classifyotu.stdout', self.an_list_files))
#define krona output files
#self.krona_files = OutputFileList(self.get_outputs('{basename_woext}.html', self.classifyotu_stdout), Formats.HTML)
#self.krona_stdout = OutputFileList(self.get_outputs('{basename_woext}.krona.stdout', self.cons_taxonomy_files))
def define_analysis(self):
self.name = "OTUAnalysis"
self.description = "Organizational Taxon Unit analysis."
self.software = "mothur"
label = "-".join(self.label)
if self.groups_files:
self.options += '#make.shared(list=FILE.an.list,group=FILE.groups,label='+self.label+');'
self.options += '#make.shared(list=FILE.an.list,group=FILE.groups,label='+label+');'
if self.count_table_files :
self.options += '#make.shared(list=FILE.an.list,count=FILE.count_table_files,label='+self.label+');'
self.options += '#summary.single(shared=FILE.shared,calc='+self.calc+',label='+self.label+');'
self.options += '#rarefaction.single(shared=FILE.shared,label='+self.label+',freq='+str(self.freq)+');'
self.options += '#make.shared(list=FILE.an.list,count=FILE.count_table_files,label='+label+');'
self.options += '#summary.single(shared=FILE.shared,calc='+self.calc+',label='+label+');'
self.options += '#rarefaction.single(shared=FILE.shared,label='+label+',freq='+str(self.freq)+');'
self.options += '#tree.shared(shared=FILE.shared,calc='+self.tree_calc+',label='+self.tree_label+');'
if self.fasta_subsample_files and self.count_table_files:
self.options += '#sub.sample(fasta=FILE.fasta,count=FILE.count_table);'
......@@ -186,13 +186,13 @@ class MothurOTUAnalysis(Analysis):
elif self.an_list_files and not self.count_table_files:
self.options += '#sub.sample(list=FILE.list);'
if self.names_files and not self.groups_files:
self.options += '#classify.otu(list=FILE.list,taxonomy=FILE.taxonomy,name=FILE.names,label='+str(self.label)+');'
self.options += '#classify.otu(list=FILE.list,taxonomy=FILE.taxonomy,name=FILE.names,label='+str(label)+');'
elif self.names_files and self.groups_files:
self.options += '#classify.otu(list=FILE.list,taxonomy=FILE.taxonomy,name=FILE.names,group=$4,label='+str(self.label)+');'
self.options += '#classify.otu(list=FILE.list,taxonomy=FILE.taxonomy,name=FILE.names,group=$4,label='+str(label)+');'
elif self.count_table_files:
self.options += '#classify.otu(list=FILE.list,taxonomy=FILE.taxonomy,count=FILE.count_table,label='+str(self.label)+');'
self.options += '#classify.otu(list=FILE.list,taxonomy=FILE.taxonomy,count=FILE.count_table,label='+str(label)+');'
else:
self.options += '#classify.otu(list=FILE.list,taxonomy=FILE.taxonomy,label='+str(self.label)+');'
self.options += '#classify.otu(list=FILE.list,taxonomy=FILE.taxonomy,label='+str(label)+');'
self.options += 'ImportMothurTaxonomy.pl '+" ".join([os.path.basename(tax) for tax in self.cons_taxonomy_files])+' -o FILE.html;'
def get_version(self):
......@@ -355,20 +355,21 @@ class MothurOTUAnalysis(Analysis):
#self._create_and_archive(result_files, archive_name)
def process(self):
label = "-".join(self.label)
#Divertsity
if self.groups_files :
makeshared = ShellFunction(self.get_exec_path("mothur") + ' "#make.shared(list=$1,group=$2,label='+self.label+',outputdir='+self.output_directory+'/)" > $3',\
makeshared = ShellFunction(self.get_exec_path("mothur") + ' "#make.shared(list=$1,group=$2,label='+label+',outputdir='+self.output_directory+'/)" > $3',\
cmd_format='{EXE} {IN} {OUT}')
makeshared = MultiMap(makeshared, inputs=[self.an_list_files,self.groups_files], outputs=[self.makeshared_stdout,self.shared_files])
if self.count_table_files :
makeshared = ShellFunction(self.get_exec_path("mothur") + ' "#make.shared(list=$1,count=$2,label='+self.label+',outputdir='+self.output_directory+'/)" > $3',\
makeshared = ShellFunction(self.get_exec_path("mothur") + ' "#make.shared(list=$1,count=$2,label='+label+',outputdir='+self.output_directory+'/)" > $3',\
cmd_format='{EXE} {IN} {OUT}')
makeshared = MultiMap(makeshared, inputs=[self.an_list_files,self.count_table_files], outputs=[self.makeshared_stdout,self.shared_files])
# Alpha diversity analysis
summarysingle = ShellFunction(self.get_exec_path("mothur") + ' "#summary.single(shared=$1,calc='+self.calc+',label='+self.label+',outputdir='+\
summarysingle = ShellFunction(self.get_exec_path("mothur") + ' "#summary.single(shared=$1,calc='+self.calc+',label='+label+',outputdir='+\
self.output_directory+'/)" > $2',cmd_format='{EXE} {IN} {OUT}')
summarysingle = MultiMap(summarysingle, inputs=[self.shared_files], outputs=[self.summarysingle_stdout,self.summary_single_files])
rarefactionsingle = ShellFunction(self.get_exec_path("mothur") + ' "#rarefaction.single(shared=$1,label='+self.label+',freq='+str(self.freq)+',outputdir='+\
rarefactionsingle = ShellFunction(self.get_exec_path("mothur") + ' "#rarefaction.single(shared=$1,label='+label+',freq='+str(self.freq)+',outputdir='+\
self.output_directory+'/)" > $2',cmd_format='{EXE} {IN} {OUT}')
rarefactionsingle = MultiMap(rarefactionsingle, inputs=[self.shared_files], outputs=[self.rarefactionsingle_stdout,self.rarefaction_single_files])
# Beta diversity analysis
......@@ -391,18 +392,18 @@ class MothurOTUAnalysis(Analysis):
subsample = MultiMap(subsample, inputs=[self.an_list_files], outputs=[self.subsample_stdout,self.subsample_list_files])
if self.names_files and not self.groups_files:
classifyotu = ShellFunction(self.get_exec_path("mothur") + ' "#classify.otu(list=$1,taxonomy=$2,name=$3,outputdir='+self.output_directory+'/,\
label='+str(self.label)+')" > $4',cmd_format='{EXE} {IN} {OUT}')
label='+str(label)+')" > $4',cmd_format='{EXE} {IN} {OUT}')
classifyotu = MultiMap(classifyotu, inputs=[self.an_list_files,self.taxonomy_files,self.names_files,], outputs=[self.classifyotu_stdout])
elif self.names_files and self.groups_files:
classifyotu = ShellFunction(self.get_exec_path("mothur") + ' "#classify.otu(list=$1,taxonomy=$2,name=$3,group=$4,outputdir='+self.output_directory+'/,\
label='+str(self.label)+')" > $5',cmd_format='{EXE} {IN} {OUT}')
label='+str(label)+')" > $5',cmd_format='{EXE} {IN} {OUT}')
classifyotu = MultiMap(classifyotu, inputs=[self.an_list_files,self.taxonomy_files,self.names_files,self.groups_files], outputs=[self.classifyotu_stdout])
elif self.count_table_files:
classifyotu = ShellFunction(self.get_exec_path("mothur") + ' "#classify.otu(list=$1,taxonomy=$2,count=$3,outputdir='+self.output_directory+'/,\
label='+str(self.label)+')" > $4',cmd_format='{EXE} {IN} {OUT}')
label='+str(label)+')" > $4',cmd_format='{EXE} {IN} {OUT}')
classifyotu = MultiMap(classifyotu, inputs=[self.an_list_files,self.taxonomy_files,self.count_table_files,], outputs=[self.classifyotu_stdout])
else:
classifyotu = ShellFunction(self.get_exec_path("mothur") + ' "#classify.otu(list=$1,taxonomy=$2,outputdir='+self.output_directory+'/,label='+str(self.tree_label)+')"\
classifyotu = ShellFunction(self.get_exec_path("mothur") + ' "#classify.otu(list=$1,taxonomy=$2,outputdir='+self.output_directory+'/,label='+str(label)+')"\
> $3',cmd_format='{EXE} {IN} {OUT}')
classifyotu = MultiMap(classifyotu, inputs=[self.an_list_files,self.taxonomy_files], outputs=[self.classifyotu_stdout])
krona = PythonFunction(get_taxonomy_to_Krona, cmd_format="{EXE} {ARG} {IN} {OUT}")
......
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