Mercurial > repos > yating-l > jbrowse_hub
changeset 48:6803152ea92a draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 073c8ceda5eddfb4ccd07cfa96a8353e5535ffaf-dirty
| author | yating-l |
|---|---|
| date | Tue, 28 Mar 2017 18:13:27 -0400 |
| parents | b7bf45272ab7 |
| children | 193e94a43f0f |
| files | TrackHub.py bedToGff3.pyc blastxmlToGff3.py blastxmlToGff3.pyc jbrowse_hub.xml tool_dependencies.xml utils.pyc |
| diffstat | 7 files changed, 10 insertions(+), 14 deletions(-) [+] |
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--- a/TrackHub.py Wed Mar 22 15:20:56 2017 -0400 +++ b/TrackHub.py Tue Mar 28 18:13:27 2017 -0400 @@ -116,8 +116,6 @@ self.createTrackList() json_file = os.path.join(self.json, "trackList.json") bigwig_track = dict() - #color_setting = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']} - #bigwig_track['style'] = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']} bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName']) bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig' @@ -128,8 +126,6 @@ #If the metadata is not set, use the default value def SetMetadata(self, track, metadata): - #print metadata - #track.update(metadata) if 'label' not in metadata.keys() or metadata['label'] == '': metadata['label'] = track['fileName'] if 'color' not in metadata.keys() or metadata['color'] == '':
--- a/blastxmlToGff3.py Wed Mar 22 15:20:56 2017 -0400 +++ b/blastxmlToGff3.py Tue Mar 28 18:13:27 2017 -0400 @@ -137,12 +137,18 @@ group['parent_field']['end'] = coords[1] group['parent_field']['score'] = group['parent_field']['strand'] = group['parent_field']['phase'] = '.' group['parent_attribute']['match_num'] = match_num + group['alignments'].sort(key=lambda x: (x['field']['start'], x['field']['end'])) utils.write_features(group['parent_field'], group['parent_attribute'], gff3) + prev_end = -1 for align in group['alignments']: + overlap = '' + if align['field']['start'] <= prev_end: + overlap += str(align['field']['start']) + ',' + str(prev_end) + prev_end = align['field']['end'] + align['attribute']['overlap'] = overlap utils.write_features(align['field'], align['attribute'], gff3) gff3.close() - def blastxml2gff3(xml_file, gff3_file): result_handle = open(xml_file) blast_records = NCBIXML.parse(result_handle)
--- a/jbrowse_hub.xml Wed Mar 22 15:20:56 2017 -0400 +++ b/jbrowse_hub.xml Tue Mar 28 18:13:27 2017 -0400 @@ -68,8 +68,6 @@ #end if #if $f.formatChoice.format_select == 'blastxml' --blastxml $f.formatChoice.BlastXML - #set track_color = str($f.formatChoice.track_color) - #silent extra_data_dict.update({"color" : $track_color}) #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict) #end if #if $f.formatChoice.format_select == 'gtf' @@ -160,13 +158,6 @@ label="Blast Alignments File" /> <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" /> - <param name="track_color" type="color" label="Track color" value="#daa520"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#"/> - </valid> - </sanitizer> - </param> </when> <when value="bigwig"> <param
--- a/tool_dependencies.xml Wed Mar 22 15:20:56 2017 -0400 +++ b/tool_dependencies.xml Tue Mar 28 18:13:27 2017 -0400 @@ -3,9 +3,11 @@ <package name="samtools" version="1.2"> <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> + <package name="numpy" version="1.9"> <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> + <package name="biopython" version="1.68"> <readme> This package is based on package_biopython_1_67 owned by biopython. @@ -45,6 +47,7 @@ </actions> </install> </package> + <package name="ucsc_tools_340" version="1.0"> <install version="1.0"> <actions_group>