comparison SAINT_preprocessing_v6_mq_pep.py @ 22:729aac64ce43 draft

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21:9e0a894d2676

# 1) infile: maxquant "Samples Report" output
# 2) baitfile: SAINT formatted bait file generated in Galaxy
# 3) prey: Y or N for generating a prey file (requires internet connection)
#######################################################################################
mq_file = sys.argv[1]
cmd = r"Rscript /home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/pre_process_protein_name_set.R " + str(mq_file) 
os.system(cmd)

infile = "./tukeys_output.txt" #maxquant "Samples Report" output
prey = sys.argv[2] # Y or N
fasta_db = sys.argv[3]
if fasta_db == "None":
    fasta_db = "/home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/SwissProt_HUMAN_2014_08.fasta"
make_bait= sys.argv[6]

def bait_create(baits, infile):
    #Takes the Bait specified by the user and makes them into a Bait file and includes a check to make sure they are using valid baits.
    baits = make_bait.split()

22:729aac64ce43

# 1) infile: maxquant "Samples Report" output
# 2) baitfile: SAINT formatted bait file generated in Galaxy
# 3) prey: Y or N for generating a prey file (requires internet connection)
#######################################################################################
mq_file = sys.argv[1]
ins_path = sys.argv[8]
names_path = str(ins_path) + r"uniprot_names.txt"
cmd = r"Rscript "+ str(ins_path) +"pre_process_protein_name_set.R " + str(mq_file) + " " + str(names_path)
os.system(cmd)

infile = "./tukeys_output.txt" #maxquant "Samples Report" output
prey = sys.argv[2] # Y or N
fasta_db = sys.argv[3]
if fasta_db == "None":
    fasta_db = str(ins_path)  + "SwissProt_HUMAN_2014_08.fasta"
make_bait= sys.argv[6]

def bait_create(baits, infile):
    #Takes the Bait specified by the user and makes them into a Bait file and includes a check to make sure they are using valid baits.
    baits = make_bait.split()