mirror of
https://github.com/galaxyproject/galaxy.git
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More work on docstrings to get them to be Sphinx compatible. Added dependency to Sphinx Makefile to get rid of errors when build files weren't there.
This commit is contained in:
Dave Clements
+15
-1
@@ -14,8 +14,22 @@ ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) sou
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# the i18n builder cannot share the environment and doctrees with the others
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I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
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# Galaxy Local variables
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TOOLDATASHAREDDIR = ../tool-data/shared
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TOOLDATABUILDFILES = $(TOOLDATASHAREDDIR)/ensembl/builds.txt \
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$(TOOLDATASHAREDDIR)/ncbi/builds.txt \
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$(TOOLDATASHAREDDIR)/ucsc/publicbuilds.txt
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.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
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# Sphinx wants the build files to be there; Copy the sample files into
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# place if we don't already have the build files.
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$(TOOLDATABUILDFILES) :
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/bin/cp $@.sample $@
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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " html to make standalone HTML files"
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@@ -41,7 +55,7 @@ help:
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clean:
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-rm -rf $(BUILDDIR)/*
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html:
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html: $(TOOLDATABUILDFILES)
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$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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@@ -25,25 +25,26 @@ class Amos( data.Text ):
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# It should call get_headers() like other sniff methods.
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"""
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Determines whether the file is an amos assembly file format
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Example:
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{CTG
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iid:1
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eid:1
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seq:
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CCTCTCCTGTAGAGTTCAACCGA-GCCGGTAGAGTTTTATCA
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.
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qlt:
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DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
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.
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{TLE
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src:1027
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off:0
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clr:618,0
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gap:
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250 612
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.
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}
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}
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Example::
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{CTG
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iid:1
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eid:1
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seq:
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CCTCTCCTGTAGAGTTCAACCGA-GCCGGTAGAGTTTTATCA
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.
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qlt:
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DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
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.
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{TLE
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src:1027
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off:0
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clr:618,0
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gap:
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250 612
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.
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}
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}
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"""
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isAmos = False
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try:
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@@ -68,7 +69,8 @@ class Sequences( sequence.Fasta ):
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def sniff( self, filename ):
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"""
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Determines whether the file is a velveth produced fasta format
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The id line has 3 fields separated by tabs: sequence_name sequence_index cataegory
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The id line has 3 fields separated by tabs: sequence_name sequence_index cataegory::
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>SEQUENCE_0_length_35 1 1
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GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT
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>SEQUENCE_1_length_35 2 1
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@@ -103,7 +105,7 @@ class Roadmaps( data.Text ):
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def sniff( self, filename ):
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"""
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Determines whether the file is a velveth produced RoadMap
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Determines whether the file is a velveth produced RoadMap::
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142858 21 1
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ROADMAP 1
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ROADMAP 2
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@@ -797,13 +797,14 @@ def get_test_fname( fname ):
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path, name = os.path.split(__file__)
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full_path = os.path.join( path, 'test', fname )
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return full_path
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def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=[] ):
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"""
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Returns the first LINE_COUNT lines wrapped to WIDTH
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Returns the first LINE_COUNT lines wrapped to WIDTH::
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## >>> fname = get_test_fname('4.bed')
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## >>> get_file_peek(fname)
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## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n'
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## >>> fname = get_test_fname('4.bed')
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## >>> get_file_peek(fname)
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## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n'
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"""
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# Set size for file.readline() to a negative number to force it to
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# read until either a newline or EOF. Needed for datasets with very
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@@ -67,14 +67,18 @@ class GenomeGraphs( Tabular ):
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"""
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from the ever-helpful angie hinrichs angie@soe.ucsc.edu
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a genome graphs call looks like this
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http://genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGenome_dataSetName=dname
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&hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess
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&hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess
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&hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals=
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&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://galaxy.esphealth.org/datasets/333/display/index
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&hgGenome_doSubmitUpload=submit
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Galaxy gives this for an interval file
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Galaxy gives this for an interval file
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http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.customText=
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http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D339%26display_app%3Ducsc
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"""
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ret_val = []
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ggtail = 'hgGenome_doSubmitUpload=submit'
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@@ -25,11 +25,14 @@ class SequenceSplitLocations( data.Text ):
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"""
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Class storing information about a sequence file composed of multiple gzip files concatenated as
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one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end.
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The format of the file is JSON:
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{ "sections" : [
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{ "start" : "x", "end" : "y", "sequences" : "z" },
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...
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]}
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The format of the file is JSON::
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{ "sections" : [
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{ "start" : "x", "end" : "y", "sequences" : "z" },
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...
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]}
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"""
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def set_peek( self, dataset, is_multi_byte=False ):
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if not dataset.dataset.purged:
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@@ -224,12 +227,19 @@ class Fasta( Sequence ):
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For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml
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Rules for sniffing as True:
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We don't care about line length (other than empty lines).
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The first non-empty line must start with '>' and the Very Next line.strip() must have sequence data and not be a header.
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'sequence data' here is loosely defined as non-empty lines which do not start with '>'
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This will cause Color Space FASTA (csfasta) to be detected as True (they are, after all, still FASTA files - they have a header line followed by sequence data)
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Previously this method did some checking to determine if the sequence data had integers (presumably to differentiate between fasta and csfasta)
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This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta
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We will only check that the first purported sequence is correctly formatted.
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>>> fname = get_test_fname( 'sequence.maf' )
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