| Previous changeset 28:dbd1af88f060 (2016-04-26) Next changeset 30:e6e456d3ac14 (2016-04-26) |
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modified:
SAINT_preprocessing_mq_pep.py |
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| diff -r dbd1af88f060 -r bd71998aec8d SAINT_preprocessing_mq_pep.py --- a/SAINT_preprocessing_mq_pep.py Tue Apr 26 14:42:16 2016 -0400 +++ b/SAINT_preprocessing_mq_pep.py Tue Apr 26 15:40:35 2016 -0400 |
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| @@ -31,15 +31,22 @@ 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) +fasta_db = sys.argv[3] + +# Uses faster names list for filtering when default db used. +if fasta_db == "None": + cmd = (r"Rscript "+ str(ins_path) +"pre_process_protein_name_set.R " + str(mq_file) + + " " + str(names_path)) + os.system(cmd) +else: + cmd = (r"Rscript "+ str(ins_path) +"pre_process_protein_name_set.R " + str(mq_file) + + " " + str(fasta_db) + os.system(cmd) infile = "./tukeys_output.txt" # The MaxQuant "Samples Report" output. prey = sys.argv[2] # Y or N boolean from Galaxy. -fasta_db = sys.argv[3] if fasta_db == "None": fasta_db = str(ins_path) + "SwissProt_HUMAN_2014_08.fasta" make_bait = sys.argv[6] |