Mercurial > repos > bornea > saint_preprocessing_peptideshaker

comparison Protein_report_processing.py @ 5:39e772aa6e93 draft

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author bornea
date Tue, 23 Aug 2016 19:06:34 -0400
parents 5a67d55bb091
children e1d6909836cd
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4:f4f75ab3e096 5:39e772aa6e93
10 quant_type = sys.argv[3] # what metric to use for quantification 10 quant_type = sys.argv[3] # what metric to use for quantification
11 # "#Validated Peptides", "#Peptides", "#Unique", "#Validated PSMs", "#PSMs" 11 # "#Validated Peptides", "#Peptides", "#Unique", "#Validated PSMs", "#PSMs"
12 db = sys.argv[4] # fasta database used in SearchGUI and PeptideShaker 12 db = sys.argv[4] # fasta database used in SearchGUI and PeptideShaker
13 prey = sys.argv[5] 13 prey = sys.argv[5]
14 tool_path = sys.argv[7] 14 tool_path = sys.argv[7]
15 if fasta_db == "None": 15 if db == "None":
16 fasta_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, infile):
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.