[2] | 1 | # before running the qc, need to rename various output files |
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| 2 | import time,string |
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| 3 | |
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| 4 | def timenow(): |
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| 5 | """return current time as a string |
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| 6 | """ |
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| 7 | return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) |
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| 8 | |
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| 9 | def get_out_formats(): |
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| 10 | """return options for formats""" |
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| 11 | dat = [['ucsc genome graphs','gg',True],['ucsc track','wig',False],['tab delimited','xls',False]] |
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| 12 | dat = [(x[0],x[1],x[2]) for x in dat] |
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| 13 | return dat |
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| 14 | |
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| 15 | |
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| 16 | def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): |
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| 17 | """Sets the name of the data |
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| 18 | <command interpreter="python2.4"> |
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| 19 | rgTDT.py -i $i.extra_files_path/$i.metadata.base_name -o $title -f $outformat -r $out_file1 -l $logf |
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| 20 | </command> |
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| 21 | |
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| 22 | """ |
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| 23 | dbk = param_dict.get('dbkey','hg18') |
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| 24 | job_name = param_dict.get( 'title1', 'rgTDTtest1' ) |
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| 25 | killme=string.punctuation+string.whitespace |
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| 26 | trantab = string.maketrans(killme,'_'*len(killme)) |
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| 27 | job_name = job_name.encode().translate(trantab) |
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| 28 | outxls = ['tabular','%s_TDT.xls' % job_name] |
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| 29 | logtxt = ['txt','%s_TDT_log.txt' % job_name] |
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| 30 | ggout = ['gg','%s_TDT_topTable.gff' % job_name] |
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| 31 | lookup={} |
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| 32 | lookup['out_file1'] = outxls |
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| 33 | lookup['logf'] = logtxt |
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| 34 | lookup['gffout'] = ggout |
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| 35 | info = 'rgTDT run at %s' % timenow() |
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| 36 | for name in lookup.keys(): |
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| 37 | data = out_data[name] |
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| 38 | data_type,newname = lookup[name] |
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| 39 | data.name = newname |
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| 40 | data.info = info |
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| 41 | data.dbkey = dbk |
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| 42 | out_data[name] = data |
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| 43 | app.model.context.flush() |
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