Mercurial > repos > bornea > saint_preprocessing

comparison SAINT_preprocessing_mq_pep.py @ 29:bd71998aec8d draft

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author bornea
date Tue, 26 Apr 2016 15:40:35 -0400
parents 0fed3fc380c7
children 761e1ad2b130
comparison
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28:dbd1af88f060 29:bd71998aec8d
29 29
30 30
31 mq_file = sys.argv[1] 31 mq_file = sys.argv[1]
32 ins_path = sys.argv[8] 32 ins_path = sys.argv[8]
33 names_path = str(ins_path) + r"uniprot_names.txt" 33 names_path = str(ins_path) + r"uniprot_names.txt"
34 cmd = (r"Rscript "+ str(ins_path) +"pre_process_protein_name_set.R " + str(mq_file) + 34 fasta_db = sys.argv[3]
35 " " + str(names_path)) 35
36 os.system(cmd) 36 # Uses faster names list for filtering when default db used.
37 if fasta_db == "None":
38 cmd = (r"Rscript "+ str(ins_path) +"pre_process_protein_name_set.R " + str(mq_file) +
39 " " + str(names_path))
40 os.system(cmd)
41 else:
42 cmd = (r"Rscript "+ str(ins_path) +"pre_process_protein_name_set.R " + str(mq_file) +
43 " " + str(fasta_db)
44 os.system(cmd)
37 45
38 infile = "./tukeys_output.txt" 46 infile = "./tukeys_output.txt"
39 # The MaxQuant "Samples Report" output. 47 # The MaxQuant "Samples Report" output.
40 prey = sys.argv[2] 48 prey = sys.argv[2]
41 # Y or N boolean from Galaxy. 49 # Y or N boolean from Galaxy.
42 fasta_db = sys.argv[3]
43 if fasta_db == "None": 50 if fasta_db == "None":
44 fasta_db = str(ins_path) + "SwissProt_HUMAN_2014_08.fasta" 51 fasta_db = str(ins_path) + "SwissProt_HUMAN_2014_08.fasta"
45 make_bait = sys.argv[6] 52 make_bait = sys.argv[6]
46 bait_bool = sys.argv[9] 53 bait_bool = sys.argv[9]
47 54