1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/71031bf3105c/ changeset: 71031bf3105c user: jgoecks date: 2012-02-14 18:27:47 summary: Better error message when bias correction/sequence data cannot be used in Cufflinks/compare/merge/diff. affected #: 5 files diff -r 33c780b4c1455628ec135b0ba98e285efcb89ed8 -r 71031bf3105c6557256bf2957ef5565ad672355d tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py +++ b/tools/ngs_rna/cuffcompare_wrapper.py @@ -58,16 +58,21 @@ # Set/link to sequence file. if options.use_seq_data: - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) if options.ref_file != 'None': + # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) + else: + # Sequence data from loc file. + cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) + if not os.path.exists( cached_seqs_pointer_file ): + stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) + # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, + # and the equCab2.fa file will contain fasta sequences. + seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) + if seq_path == '': + stop_err( 'No sequence data found for dbkey %s, so sequence data cannot be used.' % options.dbkey ) # Build command. diff -r 33c780b4c1455628ec135b0ba98e285efcb89ed8 -r 71031bf3105c6557256bf2957ef5565ad672355d tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -121,16 +121,21 @@ # If doing bias correction, set/link to sequence file. if options.do_bias_correction: - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) if options.ref_file != 'None': + # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = os.path.join( tmp_output_dir, "ref.fa" ) os.symlink( options.ref_file, seq_path ) + else: + # Sequence data from loc file. + cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) + if not os.path.exists( cached_seqs_pointer_file ): + stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) + # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, + # and the equCab2.fa file will contain fasta sequences. + seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) + if seq_path == '': + stop_err( 'No sequence data found for dbkey %s, so bias correction cannot be used.' % options.dbkey ) # Build command. diff -r 33c780b4c1455628ec135b0ba98e285efcb89ed8 -r 71031bf3105c6557256bf2957ef5565ad672355d tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -96,8 +96,8 @@ </param><conditional name="bias_correction"><param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> + <option value="No">No</option><option value="Yes">Yes</option> - <option value="No">No</option></param><when value="Yes"><conditional name="seq_source"> diff -r 33c780b4c1455628ec135b0ba98e285efcb89ed8 -r 71031bf3105c6557256bf2957ef5565ad672355d tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -79,16 +79,21 @@ # If doing bias correction, set/link to sequence file. if options.do_bias_correction: - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) if options.ref_file != 'None': + # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" - os.symlink( options.ref_file, seq_path ) + os.symlink( options.ref_file, seq_path ) + else: + # Sequence data from loc file. + cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) + if not os.path.exists( cached_seqs_pointer_file ): + stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) + # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, + # and the equCab2.fa file will contain fasta sequences. + seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) + if seq_path == '': + stop_err( 'No sequence data found for dbkey %s, so bias correction cannot be used.' % options.dbkey ) # Build command. diff -r 33c780b4c1455628ec135b0ba98e285efcb89ed8 -r 71031bf3105c6557256bf2957ef5565ad672355d tools/ngs_rna/cuffmerge_wrapper.py --- a/tools/ngs_rna/cuffmerge_wrapper.py +++ b/tools/ngs_rna/cuffmerge_wrapper.py @@ -59,16 +59,21 @@ # Set/link to sequence file. if options.use_seq_data: - cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) if options.ref_file != 'None': + # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) + else: + # Sequence data from loc file. + cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) + if not os.path.exists( cached_seqs_pointer_file ): + stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) + # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, + # and the equCab2.fa file will contain fasta sequences. + seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) + if seq_path == '': + stop_err( 'No sequence data found for dbkey %s, so sequence data cannot be used.' % options.dbkey ) # Build command. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.