Mercurial > repos > bornea > saint_preprocessing

comparison Protein_report_processing.py @ 77:4ea4e1ea75b5 draft

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author bornea
date Thu, 02 Mar 2017 16:02:22 -0500
parents 43b9bad147df
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76:43b9bad147df 77:4ea4e1ea75b5
15 if db == "None": 15 if db == "None":
16 db = str(tool_path) + "/SwissProt_HUMAN_2015_12.fasta" 16 db = str(tool_path) + "/SwissProt_HUMAN_2015_12.fasta"
17 make_bait = sys.argv[6] 17 make_bait = sys.argv[6]
18 bait_bool = sys.argv[8] 18 bait_bool = sys.argv[8]
19 19
20 def bait_create(baits, infile): 20 def bait_create(baits):
21 # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt. 21 # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
22 baits = make_bait.split() 22 baits = make_bait.split()
23 i = 0 23 i = 0
24 bait_file_tmp = open("bait.txt", "w") 24 bait_file_tmp = open("bait.txt", "w")
25 order = [] 25 order = []
37 bait_file_tmp.write(cache_line) 37 bait_file_tmp.write(cache_line)
38 38
39 bait_file_tmp.close() 39 bait_file_tmp.close()
40 40
41 if bait_bool == 'false': 41 if bait_bool == 'false':
42 bait_create(make_bait, infile) 42 bait_create(make_bait)
43 bait = "bait.txt" 43 bait = "bait.txt"
44 else: 44 else:
45 bait_temp_file = open(sys.argv[9], 'r') 45 bait_temp_file = open(sys.argv[9], 'r')
46 bait_cache = bait_temp_file.readlines() 46 bait_cache = bait_temp_file.readlines()
47 bait_file_tmp = open("bait.txt", "wr") 47 bait_file_tmp = open("bait.txt", "wr")