Mercurial > repos > bornea > saint_preprocessing

comparison SAINT_preprocessing.py @ 14:c22c1209e65f draft

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author bornea
date Tue, 12 Apr 2016 14:55:25 -0400
parents febb6def95cb
children 876af85d782c
comparison
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13:febb6def95cb 14:c22c1209e65f
55 bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n" 55 bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
56 read_infile = open(infile, "r") 56 read_infile = open(infile, "r")
57 for input_line in read_infile: 57 for input_line in read_infile:
58 input_line = input_line.strip() 58 input_line = input_line.strip()
59 temp = input_line.split('\t') 59 temp = input_line.split('\t')
60 if "Accession Number" in str(temp): 60 bait_cache.append((number_bait, str(bait_line)))
61 if baits[i] in temp:
62 number_bait = temp.index(str(baits[i]))
63 number_bait = number_bait - 9
64 bait_cache.append((number_bait, str(bait_line)))
65 # Locates the Bait names in the column names and then sets the Baits in the
66 # correct order in the cache thus the - 9 because the baits start at the 9th
67 # column.
68 else:
69 print "Error: bad bait " + str(baits[i])
70 sys.exit()
71 else:
72 pass
73 i = i + 3 61 i = i + 3
74 62
75 bait_cache.sort() 63 bait_cache.sort()
76 for cache_line in bait_cache: 64 for cache_line in bait_cache:
77 bait_file_tmp.write(cache_line[1]) 65 bait_file_tmp.write(cache_line[1])
211 elif "_YEAST" in prot_id: 199 elif "_YEAST" in prot_id:
212 proteins.append(prot_id) 200 proteins.append(prot_id)
213 elif "_MOUSE" in prot_id: 201 elif "_MOUSE" in prot_id:
214 proteins.append(prot_id) 202 proteins.append(prot_id)
215 else: 203 else:
216 print "Accession must be uniprot ID or gene name" 204 print "Accession must be uniprot ID or gene"
217 return ReturnValue2(data, proteins, header) 205 return ReturnValue2(data, proteins, header)
218 206
219 207
220 def make_inter(Scaffold_input): 208 def make_inter(Scaffold_input):
221 bait = readtab(baitfile) 209 bait = readtab(baitfile)