/tools/emboss_5/emboss_format_corrector.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 53 lines · 36 code · 5 blank · 12 comment · 9 complexity · 04460cb400af133c4c7248106669b5b7 MD5 · raw file
- #EMBOSS format corrector
- import operator
- #from galaxy import datatypes
- #Properly set file formats after job run
- def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr):
- #Properly set file formats before job run
- #def exec_before_job(trans, inp_data, out_data, param_dict,tool):
- #why isn't items an ordered list?
- items = out_data.items()
- #lets sort it ourselves....
- items = sorted(items, key=operator.itemgetter(0))
- #items is now sorted...
-
- #normal filetype correction
- data_count=1
- for name, data in items:
- outputType = param_dict.get( 'out_format'+str(data_count), None )
- #print "data_count",data_count, "name", name, "outputType", outputType
- if outputType !=None:
- if outputType == 'ncbi':
- outputType = "fasta"
- elif outputType == 'excel':
- outputType = "tabular"
- elif outputType == 'text':
- outputType = "txt"
- data = app.datatypes_registry.change_datatype(data, outputType)
- app.model.context.add( data )
- app.model.context.flush()
- data_count+=1
-
- #html filetype correction
- data_count=1
- for name, data in items:
- wants_plot = param_dict.get( 'html_out'+str(data_count), None )
- ext = "html"
- if wants_plot == "yes":
- data = app.datatypes_registry.change_datatype(data, ext)
- app.model.context.add( data )
- app.model.context.flush()
- data_count+=1
-
- #png file correction
- data_count=1
- for name, data in items:
- wants_plot = param_dict.get( 'plot'+str(data_count), None )
- ext = "png"
- if wants_plot == "yes":
- data = app.datatypes_registry.change_datatype(data, ext)
- app.model.context.add( data )
- app.model.context.flush()
- data_count+=1