/tools/rgenetics/rgGRR_code.py
Python | 37 lines | 31 code | 2 blank | 4 comment | 5 complexity | 8ef80cf450578576021dc0ed954fc054 MD5 | raw file
1from galaxy import datatypes,model 2import sys,time,string,os,shutil 3 4def timenow(): 5 """return current time as a string 6 """ 7 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) 8 9def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): 10 """Sets the name of the html output file 11 """ 12 killme = string.punctuation + string.whitespace 13 trantab = string.maketrans(killme,'_'*len(killme)) 14 job_name = param_dict.get( 'title1', 'rgGRR' ) 15 job_name = job_name.encode() 16 newname = '%s.html' % job_name.translate(trantab) 17 indatname = inp_data['i'].name 18 info = '%s Mean allele sharing on %s at %s' % (job_name,indatname,timenow()) 19 ofname = 'out_file1' 20 data = out_data[ofname] 21 data.name = newname 22 data.info = info 23 out_data[ofname] = data 24 fromdir = data.extra_files_path 25 indat = inp_data['i'] 26 indatname = indat.name 27 base_name = indat.metadata.base_name 28 todir = indat.extra_files_path # where the ldreduced stuff should be 29 ldfname = '%s_INDEP_THIN' % base_name # we store ld reduced and thinned data 30 ldout = os.path.join(todir,ldfname) 31 ldin = os.path.join(fromdir,ldfname) 32 if os.path.exists('%s.bed' % ldin) and not os.path.exists('%s.bed' % ldout): # copy ldreduced to input for next time 33 for ext in ['bim','bed','fam']: 34 src = '%s.%s' % (ldin,ext) 35 dest = '%s.%s' % (ldout,ext) 36 shutil.copy(src,dest) 37 app.model.context.flush()