Mercurial > repos > peterjc > tmhmm_and_signalp
changeset 8:976a5f2833cd draft
Uploaded v0.1.1 of the bundle, which fixes an error in the header of the tabular output produced for Promoter 2.0
| author | peterjc |
|---|---|
| date | Mon, 30 Jul 2012 12:56:54 -0400 |
| parents | 9b45a8743100 |
| children | e52220a9ddad |
| files | tools/protein_analysis/README tools/protein_analysis/promoter2.py tools/protein_analysis/promoter2.xml |
| diffstat | 3 files changed, 4 insertions(+), 5 deletions(-) [+] |
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--- a/tools/protein_analysis/README Mon Jul 30 10:25:07 2012 -0400 +++ b/tools/protein_analysis/README Mon Jul 30 12:56:54 2012 -0400 @@ -126,6 +126,7 @@ v0.0.9 - Added our RXLR motifs tool to the suite. v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers) - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter +v0.1.1 - Fixed an error in the header of the tabular output from Promoter Developers ==========
--- a/tools/protein_analysis/promoter2.py Mon Jul 30 10:25:07 2012 -0400 +++ b/tools/protein_analysis/promoter2.py Mon Jul 30 12:56:54 2012 -0400 @@ -73,7 +73,6 @@ """Parse text output into tabular, return query count.""" identifier = None queries = 0 - #out.write("#Identifier\tDescription\tPosition\tScore\tLikelihood\n") for line in raw_handle: #print repr(line) if not line.strip() or line == "Promoter prediction:\n": @@ -99,7 +98,6 @@ "Highly likely prediction"]: stop_err("ERROR: Problem with line: %r" % line) out_handle.write("%s\t%s\t%s\t%s\n" % (identifier, position, score, likelihood)) - #out.close() return queries working_dir, bin = get_path_and_binary() @@ -147,7 +145,7 @@ del jobs out_handle = open(tabular_file, "w") -out_handle.write("#Identifier\tDescription\tPosition\tScore\tLikelihood\n") +out_handle.write("#Identifier\tPosition\tScore\tLikelihood\n") queries = 0 for temp in temp_files: data_handle = open(temp)
--- a/tools/protein_analysis/promoter2.xml Mon Jul 30 10:25:07 2012 -0400 +++ b/tools/protein_analysis/promoter2.xml Mon Jul 30 12:56:54 2012 -0400 @@ -1,4 +1,4 @@ -<tool id="promoter2" name="Promoter 2.0" version="0.0.1"> +<tool id="promoter2" name="Promoter 2.0" version="0.0.2"> <description>Find eukaryotic PolII promoters in DNA sequences</description> <!-- If job splitting is enabled, break up the query file into parts --> <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal --> @@ -22,7 +22,7 @@ **What it does** -This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoters sequences using a Neural Network (NN) model. +This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model. The input is a FASTA file of nucleotide sequences (e.g. upstream regions of your genes), and the output is tabular with five columns (one row per promoter):