Mercurial > repos > bornea > query_crapome

comparison CRAPomeQuery.py @ 8:6fe48eb42c55 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bornea
date Mon, 18 Apr 2016 12:23:24 -0400
parents d1a26feef9de
children 577611df296d
comparison
equal deleted inserted replaced
7:9c72c51d858d 8:6fe48eb42c55
2 """ 2 """
3 Created on Thu Apr 14 16:58:05 2016 3 Created on Thu Apr 14 16:58:05 2016
4 4
5 @author: brentkuenzi 5 @author: brentkuenzi
6 """ 6 """
7 ################################################################################
8 ## Dependencies ##
9 import urllib2
10 import sys
11 import numpy
12 import os
7 ################################################################################ 13 ################################################################################
8 # This program will read in a SAINT formatted 'prey.txt' file or a file 14 # This program will read in a SAINT formatted 'prey.txt' file or a file
9 # containing a single column list of uniprot accessions (e.g. "P00533" or 15 # containing a single column list of uniprot accessions (e.g. "P00533" or
10 # "EGFR_HUMAN")query the CRAPome database (v1.1), and return a file specifying 16 # "EGFR_HUMAN")query the CRAPome database (v1.1), and return a file specifying
11 # the prevalence of each protein in the CRAPome. 17 # the prevalence of each protein in the CRAPome.
22 # 1) crappyData: Prey.txt or single column list of Uniprot accessions 28 # 1) crappyData: Prey.txt or single column list of Uniprot accessions
23 crappyData = sys.argv[1] # Prey file or File with single column of accessions 29 crappyData = sys.argv[1] # Prey file or File with single column of accessions
24 # 2) Species: HUMAN or YEAST 30 # 2) Species: HUMAN or YEAST
25 species = sys.argv[2] # HUMAN or YEAST 31 species = sys.argv[2] # HUMAN or YEAST
26 db_path = sys.argv[4] 32 db_path = sys.argv[4]
27 ################################################################################
28 ## Dependencies ##
29 import urllib2
30 import sys
31 import numpy
32 import os
33 ################################################################################ 33 ################################################################################
34 ## Global Variables ## 34 ## Global Variables ##
35 if species == "HUMAN": 35 if species == "HUMAN":
36 database = str(db_path) + "Human_CRAPome_v1-1.txt" 36 database = str(db_path) + "Human_CRAPome_v1-1.txt"
37 if species == "YEAST": 37 if species == "YEAST":