Mercurial > repos > fubar > data_manager_rnasta
changeset 1:ebadd2c92958 draft
Uploaded
| author | fubar |
|---|---|
| date | Mon, 29 Sep 2014 20:47:45 -0400 |
| parents | 84f6e67cbae5 |
| children | 8a2d16bfdae2 |
| files | data_manager/rnastar_index_builder.py data_manager/rnastar_index_builder.xml tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/rnastar_index_builder.py Mon Sep 29 20:25:10 2014 -0400 +++ b/data_manager/rnastar_index_builder.py Mon Sep 29 20:47:45 2014 -0400 @@ -43,7 +43,7 @@ cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' % pdict elif sjdbFileChrStartEnd: - cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' + cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" ) args = cl.split(' ') proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) @@ -104,6 +104,7 @@ sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript, sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix, n_threads=options.runThreadN ) + #save info to json file open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
--- a/data_manager/rnastar_index_builder.xml Mon Sep 29 20:25:10 2014 -0400 +++ b/data_manager/rnastar_index_builder.xml Mon Sep 29 20:47:45 2014 -0400 @@ -6,7 +6,7 @@ <command interpreter="python"> rnastar_index_builder.py --out_file "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" ---data_table_name "rnastar_indexes" --out_index_path "$out_file.extra_files_path" --runThreadN 1 +--data_table_name "rnastar_indexes" --out_index_path "${out_file.extra_files_path}" --runThreadN 1 #if $genemodel.modelformat=="gff3": --sjdbOverhang "${genemodel.sjdbOverhang}" --sjdbGTFfile "${genemodel.sjdbGTFfile}"
--- a/tool_data_table_conf.xml.sample Mon Sep 29 20:25:10 2014 -0400 +++ b/tool_data_table_conf.xml.sample Mon Sep 29 20:47:45 2014 -0400 @@ -7,6 +7,6 @@ <!-- Locations of indexes in the BWA mapper format --> <table name="rnastar_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/rnastar_index.loc" /> + <file path="tool-data/rnastar_indexes.loc" /> </table> </tables>