comparison Protein_report_processing.py @ 13:fcacb3f20451 draft default tip

Uploaded

12:ad33728cecc0

import sys
import os
from time import sleep

files = sys.argv[1] # read in a string of file names seperated by ", "
print files
# e.g. "Default_Protein_Report.txt, Default_Protein_Report_2.txt"
#bait = sys.argv[2] # SAINT formatted bait file
# still need a way to match files to bait identifiers
# or they can just be required to be put in the order of the bait file
quant_type = sys.argv[3] # what metric to use for quantification
print quant_type
# "#Validated Peptides", "#Peptides", "#Unique", "#Validated PSMs", "#PSMs"
db = sys.argv[4] # fasta database used in SearchGUI and PeptideShaker
print db
prey = sys.argv[5]
print prey
tool_path = sys.argv[7]
print tool_path
if db == "None":
    db = str(tool_path)  + "/SwissProt_HUMAN_2015_12.fasta"
make_bait = sys.argv[6]
print make_bait
bait_bool = sys.argv[8]
print bait_bool

def bait_create(baits, infile):
    # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
    baits = make_bait.split()
    i = 0

if prey == "true":
    make_prey(data,db)

os.rename("bait.txt", sys.argv[2])
os.rename("inter.txt", sys.argv[10])
os.rename("prey.txt", sys.argv[11])

13:fcacb3f20451

import sys
import os
from time import sleep

files = sys.argv[1] # read in a string of file names seperated by ", "
# e.g. "Default_Protein_Report.txt, Default_Protein_Report_2.txt"
#bait = sys.argv[2] # SAINT formatted bait file
# still need a way to match files to bait identifiers
# or they can just be required to be put in the order of the bait file
quant_type = sys.argv[3] # what metric to use for quantification
# "#Validated Peptides", "#Peptides", "#Unique", "#Validated PSMs", "#PSMs"
db = sys.argv[4] # fasta database used in SearchGUI and PeptideShaker
prey = sys.argv[5]
tool_path = sys.argv[7]
if db == "None":
    db = str(tool_path)  + "/SwissProt_HUMAN_2015_12.fasta"
make_bait = sys.argv[6]
bait_bool = sys.argv[8]

def bait_create(baits, infile):
    # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
    baits = make_bait.split()
    i = 0

if prey == "true":
    make_prey(data,db)

os.rename("bait.txt", sys.argv[2])
os.rename("inter.txt", sys.argv[10])
if str(prey) != "None": 
    os.rename("prey.txt", sys.argv[11])