Mercurial > repos > bornea > saint_preproc
diff SAINT_preprocessing_v6_mq_pep.py @ 22:729aac64ce43 draft
Uploaded
| author | bornea |
|---|---|
| date | Thu, 19 Nov 2015 13:38:31 -0500 |
| parents | 9c3d2b1d0c1c |
| children |
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--- a/SAINT_preprocessing_v6_mq_pep.py Thu Nov 19 13:38:20 2015 -0500 +++ b/SAINT_preprocessing_v6_mq_pep.py Thu Nov 19 13:38:31 2015 -0500 @@ -17,14 +17,16 @@ # 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) +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 = "/home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/SwissProt_HUMAN_2014_08.fasta" + fasta_db = str(ins_path) + "SwissProt_HUMAN_2014_08.fasta" make_bait= sys.argv[6] def bait_create(baits, infile):