Mercurial > repos > devteam > emboss_5
annotate emboss_5/emboss_format_corrector.py @ 7:55075056bd56
Fix for emboss_format_corrector.py. Datatypes should be changed before the job is run.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Fri, 11 Oct 2013 14:03:31 -0400 |
| parents | d3a9c3114f2c |
| children |
| rev | line source |
|---|---|
| 0 | 1 #EMBOSS format corrector |
| 2 | |
| 3 import operator | |
| 4 | |
| 5 #Properly set file formats before job run | |
|
7
55075056bd56
Fix for emboss_format_corrector.py. Datatypes should be changed before the job is run.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
0
diff
changeset
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6 def exec_before_job( app, inp_data=None, out_data=None, tool=None, param_dict=None ): |
| 0 | 7 #why isn't items an ordered list? |
| 8 items = out_data.items() | |
| 9 #lets sort it ourselves.... | |
| 10 items = sorted(items, key=operator.itemgetter(0)) | |
| 11 #items is now sorted... | |
| 12 | |
| 13 #normal filetype correction | |
| 14 data_count=1 | |
| 15 for name, data in items: | |
| 16 outputType = param_dict.get( 'out_format'+str(data_count), None ) | |
| 17 #print "data_count",data_count, "name", name, "outputType", outputType | |
| 18 if outputType !=None: | |
| 19 if outputType == 'ncbi': | |
| 20 outputType = "fasta" | |
| 21 elif outputType == 'excel': | |
| 22 outputType = "tabular" | |
| 23 elif outputType == 'text': | |
| 24 outputType = "txt" | |
| 25 data = app.datatypes_registry.change_datatype(data, outputType) | |
| 26 app.model.context.add( data ) | |
| 27 app.model.context.flush() | |
| 28 data_count+=1 | |
| 29 | |
| 30 #html filetype correction | |
| 31 data_count=1 | |
| 32 for name, data in items: | |
| 33 wants_plot = param_dict.get( 'html_out'+str(data_count), None ) | |
| 34 ext = "html" | |
| 35 if wants_plot == "yes": | |
| 36 data = app.datatypes_registry.change_datatype(data, ext) | |
| 37 app.model.context.add( data ) | |
| 38 app.model.context.flush() | |
| 39 data_count+=1 | |
| 40 | |
| 41 #png file correction | |
| 42 data_count=1 | |
| 43 for name, data in items: | |
| 44 wants_plot = param_dict.get( 'plot'+str(data_count), None ) | |
| 45 ext = "png" | |
| 46 if wants_plot == "yes": | |
| 47 data = app.datatypes_registry.change_datatype(data, ext) | |
| 48 app.model.context.add( data ) | |
| 49 app.model.context.flush() | |
| 50 data_count+=1 |