Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_format_corrector.py @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 #EMBOSS format corrector | |
2 | |
3 import operator | |
4 #from galaxy import datatypes | |
5 | |
6 #Properly set file formats after job run | |
7 def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr): | |
8 #Properly set file formats before job run | |
9 #def exec_before_job(trans, inp_data, out_data, param_dict,tool): | |
10 #why isn't items an ordered list? | |
11 items = out_data.items() | |
12 #lets sort it ourselves.... | |
13 items = sorted(items, key=operator.itemgetter(0)) | |
14 #items is now sorted... | |
15 | |
16 #normal filetype correction | |
17 data_count=1 | |
18 for name, data in items: | |
19 outputType = param_dict.get( 'out_format'+str(data_count), None ) | |
20 #print "data_count",data_count, "name", name, "outputType", outputType | |
21 if outputType !=None: | |
22 if outputType == 'ncbi': | |
23 outputType = "fasta" | |
24 elif outputType == 'excel': | |
25 outputType = "tabular" | |
26 elif outputType == 'text': | |
27 outputType = "txt" | |
28 data = app.datatypes_registry.change_datatype(data, outputType) | |
29 app.model.context.add( data ) | |
30 app.model.context.flush() | |
31 data_count+=1 | |
32 | |
33 #html filetype correction | |
34 data_count=1 | |
35 for name, data in items: | |
36 wants_plot = param_dict.get( 'html_out'+str(data_count), None ) | |
37 ext = "html" | |
38 if wants_plot == "yes": | |
39 data = app.datatypes_registry.change_datatype(data, ext) | |
40 app.model.context.add( data ) | |
41 app.model.context.flush() | |
42 data_count+=1 | |
43 | |
44 #png file correction | |
45 data_count=1 | |
46 for name, data in items: | |
47 wants_plot = param_dict.get( 'plot'+str(data_count), None ) | |
48 ext = "png" | |
49 if wants_plot == "yes": | |
50 data = app.datatypes_registry.change_datatype(data, ext) | |
51 app.model.context.add( data ) | |
52 app.model.context.flush() | |
53 data_count+=1 |