Mercurial > repos > bornea > saint_preprocessing

comparison mzID_process2.py @ 68:a48ac530e4fe draft

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Uploaded
author bornea
date Sat, 27 Aug 2016 22:56:13 -0400
parents b8169cc0b860
children f6fbe5d6a94f
comparison
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67:b8169cc0b860 68:a48ac530e4fe
129 return ReturnValue2(inter,accessions) 129 return ReturnValue2(inter,accessions)
130 130
131 131
132 files = sys.argv[1] 132 files = sys.argv[1]
133 file_list = files.split(",") 133 file_list = files.split(",")
134 bait = read_tab(sys.argv[2]) 134
135 make_prey = sys.argv[3] 135 make_prey = sys.argv[3]
136 db = sys.argv[4] 136 db = sys.argv[4]
137 if db == "None": 137 if db == "None":
138 db = str(ins_path) + "/SwissProt_HUMAN_2015_12.fasta" 138 db = str(ins_path) + "/SwissProt_HUMAN_2015_12.fasta"
139 make_bait = sys.argv[6] 139 make_bait = sys.argv[6]
172 bait_file_tmp = open("bait.txt", "wr") 172 bait_file_tmp = open("bait.txt", "wr")
173 for cache_line in bait_cache: 173 for cache_line in bait_cache:
174 bait_file_tmp.write(cache_line) 174 bait_file_tmp.write(cache_line)
175 bait_file_tmp.close() 175 bait_file_tmp.close()
176 bait = "bait.txt" 176 bait = "bait.txt"
177 bait = read_tab("bait.txt")
177 178
178 inter = "" 179 inter = ""
179 cnt = 0 180 cnt = 0
180 accessions = [] 181 accessions = []
181 for i in file_list: 182 for i in file_list: