comparison Protein_report_processing.py @ 9:e01bdd338210 draft

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8:e1d6909836cd

# 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

        error.close
        seqlength = 'NA'
        genename = 'NA'
        return ReturnValue1(seqlength, genename)
def concatenate_files(file_list_string, bait_file):
    file_list = file_list_string.split(", ")
    bait = read_tab(bait_file)
    master_table = []
    header_check = 0
    file_cnt = 0
    table_cnt = 0

9:e01bdd338210

# 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

        error.close
        seqlength = 'NA'
        genename = 'NA'
        return ReturnValue1(seqlength, genename)
def concatenate_files(file_list_string, bait_file):
    file_list = file_list_string.split(",")
    bait = read_tab(bait_file)
    master_table = []
    header_check = 0
    file_cnt = 0
    table_cnt = 0