comparison SAINT_preprocessing.py @ 11:b688d0dae86b draft

Uploaded

10:1b0547d3c7bc

# 5) make_bait: String of bait names, assignment, and test or control boolean
#######################################################################################

import sys
import os.path


infile = sys.argv[1] 
#Scaffold "Samples Report" output.
prey = sys.argv[2] 

    # Cut off blank line and END OF FILE.
    proteins = []
    for Scaffold_line in data:
        Scaffold_line[4] = Scaffold_line[4].split()[0]
        # Removes the (+##) that sometimes is attached.
    for protein in data:
        proteins.append(protein[prot_start])
    return ReturnValue2(data, proteins, header)


def make_inter(Scaffold_input):
    bait = readtab(baitfile)

11:b688d0dae86b

# 5) make_bait: String of bait names, assignment, and test or control boolean
#######################################################################################

import sys
import os.path
import re


infile = sys.argv[1] 
#Scaffold "Samples Report" output.
prey = sys.argv[2] 

    # Cut off blank line and END OF FILE.
    proteins = []
    for Scaffold_line in data:
        Scaffold_line[4] = Scaffold_line[4].split()[0]
        # Removes the (+##) that sometimes is attached.
    uniprot_re = re.compile("[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}")
    for protein in data: 
        prot_id = uniprot_re.match(protein[prot_start])
        proteins.append(prot_id.group())
    return ReturnValue2(data, proteins, header)


def make_inter(Scaffold_input):
    bait = readtab(baitfile)