1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/b0c916349070/ changeset: b0c916349070 user: clements date: 2012-11-01 07:08:09 summary: Update docstrings so they no longer generate warnings in Sphix. affected #: 2 files

diff -r f2abe519d05e6f4e01fcf9983ab3fb72f5009272 -r b0c9163490705bd872c2877070196056bc4e872e lib/galaxy/datatypes/util/gff_util.py --- a/lib/galaxy/datatypes/util/gff_util.py +++ b/lib/galaxy/datatypes/util/gff_util.py @@ -119,12 +119,13 @@ Reader wrapper for GFF files.

Wrapper has two major functions: - (1) group entries for GFF file (via group column), GFF3 (via id attribute), - or GTF (via gene_id/transcript id); - (2) convert coordinates from GFF format--starting and ending coordinates - are 1-based, closed--to the 'traditional'/BED interval format--0 based, - half-open. This is useful when using GFF files as inputs to tools that - expect traditional interval format. + + 1. group entries for GFF file (via group column), GFF3 (via id attribute), + or GTF (via gene_id/transcript id); + 2. convert coordinates from GFF format--starting and ending coordinates + are 1-based, closed--to the 'traditional'/BED interval format--0 based, + half-open. This is useful when using GFF files as inputs to tools that + expect traditional interval format. """

def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3, \ @@ -303,9 +304,13 @@ """ Parses a GFF/GTF attribute string and returns a dictionary of name-value pairs. The general format for a GFF3 attributes string is + name1=value1;name2=value2 + The general format for a GTF attribute string is + name1 "value1" ; name2 "value2" + The general format for a GFF attribute string is a single string that denotes the interval's group; in this case, method returns a dictionary with a single key-value pair, and key name is 'group' @@ -412,4 +417,4 @@ for chrom_features in chroms_features_sorted: for feature in chrom_features: yield feature - \ No newline at end of file +

diff -r f2abe519d05e6f4e01fcf9983ab3fb72f5009272 -r b0c9163490705bd872c2877070196056bc4e872e lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -7,6 +7,7 @@ """ Compose the sequence of commands necessary to execute a job. This will currently include: + - environment settings corresponding to any requirement tags - preparing input files - command line taken from job wrapper

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