Mercurial > repos > bornea > saint_preprocessing_peptideshaker

comparison Protein_report_processing.py @ 13:fcacb3f20451 draft default tip

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author bornea
date Wed, 24 Aug 2016 12:57:25 -0400
parents 9ec349fd0e66
children
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12:ad33728cecc0 13:fcacb3f20451
1 import sys 1 import sys
2 import os 2 import os
3 from time import sleep 3 from time import sleep
4 4
5 files = sys.argv[1] # read in a string of file names seperated by ", " 5 files = sys.argv[1] # read in a string of file names seperated by ", "
6 print files
7 # e.g. "Default_Protein_Report.txt, Default_Protein_Report_2.txt" 6 # e.g. "Default_Protein_Report.txt, Default_Protein_Report_2.txt"
8 #bait = sys.argv[2] # SAINT formatted bait file 7 #bait = sys.argv[2] # SAINT formatted bait file
9 # still need a way to match files to bait identifiers 8 # still need a way to match files to bait identifiers
10 # or they can just be required to be put in the order of the bait file 9 # or they can just be required to be put in the order of the bait file
11 quant_type = sys.argv[3] # what metric to use for quantification 10 quant_type = sys.argv[3] # what metric to use for quantification
12 print quant_type
13 # "#Validated Peptides", "#Peptides", "#Unique", "#Validated PSMs", "#PSMs" 11 # "#Validated Peptides", "#Peptides", "#Unique", "#Validated PSMs", "#PSMs"
14 db = sys.argv[4] # fasta database used in SearchGUI and PeptideShaker 12 db = sys.argv[4] # fasta database used in SearchGUI and PeptideShaker
15 print db
16 prey = sys.argv[5] 13 prey = sys.argv[5]
17 print prey
18 tool_path = sys.argv[7] 14 tool_path = sys.argv[7]
19 print tool_path
20 if db == "None": 15 if db == "None":
21 db = str(tool_path) + "/SwissProt_HUMAN_2015_12.fasta" 16 db = str(tool_path) + "/SwissProt_HUMAN_2015_12.fasta"
22 make_bait = sys.argv[6] 17 make_bait = sys.argv[6]
23 print make_bait
24 bait_bool = sys.argv[8] 18 bait_bool = sys.argv[8]
25 print bait_bool
26 19
27 def bait_create(baits, infile): 20 def bait_create(baits, infile):
28 # 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.
29 baits = make_bait.split() 22 baits = make_bait.split()
30 i = 0 23 i = 0
217 if prey == "true": 210 if prey == "true":
218 make_prey(data,db) 211 make_prey(data,db)
219 212
220 os.rename("bait.txt", sys.argv[2]) 213 os.rename("bait.txt", sys.argv[2])
221 os.rename("inter.txt", sys.argv[10]) 214 os.rename("inter.txt", sys.argv[10])
222 os.rename("prey.txt", sys.argv[11]) 215 if str(prey) != "None":
216 os.rename("prey.txt", sys.argv[11])