[2] | 1 | # for caco
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| 2 | # called as plinkCaCo.py $i $name $test $outformat $out_file1 $logf $map
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| 3 | from galaxy import datatypes
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| 4 | import time,string,sys
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| 5 |
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| 6 | def timenow():
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| 7 | """return current time as a string
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| 8 | """
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| 9 | return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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| 10 |
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| 11 | def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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| 12 | """Sets the name of the data"""
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| 13 | job_name = param_dict.get( 'name', 'RgCaCo' ).encode()
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| 14 | killme = string.punctuation + string.whitespace
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| 15 | trantab = string.maketrans(killme,'_'*len(killme))
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| 16 | title = job_name.translate(trantab)
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| 17 | indatname = inp_data['i'].name
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| 18 | outxls = ['tabular','%s_CaCo.xls' % job_name]
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| 19 | logtxt = ['txt','%s_CaCo_log.txt' % job_name]
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| 20 | ggout = ['gff','%s_CaCo_topTable.gff' % job_name]
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| 21 | lookup={}
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| 22 | lookup['out_file1'] = outxls
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| 23 | lookup['logf'] = logtxt
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| 24 | lookup['gffout'] = ggout
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| 25 | info = '%s rgCaCo from %s at %s' % (job_name,indatname,timenow())
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| 26 | for name in lookup.keys():
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| 27 | data = out_data[name]
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| 28 | data_type,newname = lookup[name]
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| 29 | data.name = newname
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| 30 | data.info = info
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| 31 | out_data[name] = data
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| 32 | app.model.context.flush()
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| 33 |
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| 34 |
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| 35 | def get_test_opts():
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| 36 | """return test options"""
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| 37 | dat = [('Armitage test for trend chisq. Does NOT assume HWE!','TREND',True),
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| 38 | ('Allelic (A vs a) chisq. assumes HWE','ALLELIC',False),
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| 39 | ('Genotype (AA vs Aa vs aa)chisq. assumes HWE','GENO',False),
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| 40 | ('Dominant model (AA/Aa vs aa) chisq. assumesWE','DOM',False),
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| 41 | ('Recessive (AA vs Aa/aa) chisq. assumes HWE','REC',False)]
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| 42 | dat.reverse()
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| 43 | return dat
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| 44 |
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| 45 |
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