Mercurial > repos > bornea > saint_preprocessing

comparison mzID_process2.py @ 73:50391fdc229a draft

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Uploaded
author bornea
date Sat, 27 Aug 2016 23:37:08 -0400
parents 5ec0b997fb13
children 211fd8ae6edc
comparison
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72:5ec0b997fb13 73:50391fdc229a
182 for i in file_list: 182 for i in file_list:
183 cmd = (r"Rscript "+ str(ins_path) +"flatten_mzIdentML.R " + i) 183 cmd = (r"Rscript "+ str(ins_path) +"flatten_mzIdentML.R " + i)
184 os.system(cmd) 184 os.system(cmd)
185 mzIdentML = read_tab("flat_mzIdentML.txt") 185 mzIdentML = read_tab("flat_mzIdentML.txt")
186 inter = inter + make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).inter 186 inter = inter + make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).inter
187 print inter
188 accessions.append(make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).accessions) 187 accessions.append(make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).accessions)
189 print accessions
190 cnt+=1 188 cnt+=1
191 189
192 with open("inter.txt","w") as x: 190 with open("inter.txt","w") as x:
193 x.write(inter) 191 x.write(inter)
194 if make_prey == "Y": 192 if make_prey == "true":
195 unique_accessions = [] 193 unique_accessions = []
196 prey = "" 194 prey = ""
197 for i in accessions: 195 for i in accessions:
198 for j in i: 196 for j in i:
199 if j not in unique_accessions: 197 if j not in unique_accessions: