Mercurial > repos > yating-l > jbrowse_hub
changeset 39:75edbc203532 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
| author | yating-l |
|---|---|
| date | Fri, 17 Mar 2017 19:00:01 -0400 |
| parents | 3a3591cf27f9 |
| children | 4af741177682 |
| files | TrackHub.py jbrowse_hub.py jbrowse_hub.xml trackObject.py |
| diffstat | 4 files changed, 43 insertions(+), 37 deletions(-) [+] |
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--- a/TrackHub.py Fri Mar 17 16:28:21 2017 -0400 +++ b/TrackHub.py Fri Mar 17 19:00:01 2017 -0400 @@ -46,7 +46,12 @@ def addTrack(self, track): track_label = track['label'] track_color = track['track_color'] - track_type = track['track_type'] + if track['dataType'] == 'blastxml': + track_type = "G-OnRamp_plugin/BlastAlignment" + elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna': + track_type = "G-OnRamp_plugin/GenePred" + else: + track_type = "CanvasFeatures" if track['dataType'] == 'bam': self.createTrackList() json_file = os.path.join(self.json, "trackList.json") @@ -54,7 +59,6 @@ bam_track['type'] = 'JBrowse/View/Track/Alignments2' bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' bam_track['label'] = track_label - bam_track['color'] = track_color bam_track['urlTemplate'] = os.path.join('../raw', track['fileName']) bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index']) utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') @@ -64,7 +68,8 @@ json_file = os.path.join(self.json, "trackList.json") bigwig_track = dict() bigwig_track['label'] = track_label - bigwig_track['color'] = track_color + #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' @@ -72,15 +77,11 @@ else: gff3_file = os.path.join(self.raw, track['fileName']) if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf': - p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments", "color" : "%s"}' % track_color, '--out', self.json]) + p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--Config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments"}', '--clientConfig', '{"color" : "%s"}' % track_color, '--out', self.json]) elif track['dataType'] == 'gff3_transcript': - p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"transcriptType": "transcript", "color" : "%s"}' % track_color, '--out', self.json]) - elif track['dataType'] == 'gff3_mrna': - p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"color" : "%s"}' % track_color, '--out', self.json]) - elif track['dataType'] == 'blastxml': - p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"color" : "%s"}' % track_color, '--out', self.json]) + p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--Config', '{"transcriptType": "transcript"}', '--clientConfig', '{"color" : "%s"}' % track_color, '--out', self.json]) else: - p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"color" : "%s"}' % track_color, '--out', self.json]) + p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--clientConfig', '{"color" : "%s"}' % track_color, '--out', self.json]) p.communicate() def indexName(self):
--- a/jbrowse_hub.py Fri Mar 17 16:28:21 2017 -0400 +++ b/jbrowse_hub.py Fri Mar 17 19:00:01 2017 -0400 @@ -132,7 +132,7 @@ #print f if f in inputs_data.keys(): metadata = inputs_data[f] - #print metadata + print metadata #Convert tracks into gff3 format all_tracks.addToRaw(f, datatype, metadata)
--- a/jbrowse_hub.xml Fri Mar 17 16:28:21 2017 -0400 +++ b/jbrowse_hub.xml Fri Mar 17 19:00:01 2017 -0400 @@ -38,10 +38,10 @@ #for $f in $format #set track_label = str($f.formatChoice.label) - #set track_color = str($f.formatChoice.track_color) - #set extra_data_dict = {"label" : $track_label, - "track_color" : $track_color} + #set extra_data_dict = {"label" : $track_label} #if $f.formatChoice.format_select == 'bed' + #set track_color = str($f.formatChoice.track_color) + #silent extra_data_dict.update({"track_color" : $track_color}) #if $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option' --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict) @@ -55,8 +55,8 @@ #silent $prepare_json($f.formatChoice.BAM, extra_data_dict) #end if #if $f.formatChoice.format_select == 'gff3' - #set track_type = $f.formatChoice.track_type - #silent extra_data_dict.update({"track_type" : $track_type}) + #set track_color = str($f.formatChoice.track_color) + #silent extra_data_dict.update({"track_color" : $track_color}) #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript' --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict) @@ -66,17 +66,22 @@ #end if #end if #if $f.formatChoice.format_select == 'blastxml' - #set track_type = $f.formatChoice.track_type - #silent extra_data_dict.update({"track_type" : $track_type}) --blastxml $f.formatChoice.BlastXML + #set track_color = str($f.formatChoice.track_color) + #silent extra_data_dict.update({"track_color" : $track_color}) #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict) #end if #if $f.formatChoice.format_select == 'gtf' --gtf $f.formatChoice.GTF + #set track_color = str($f.formatChoice.track_color) + #silent extra_data_dict.update({"track_color" : $track_color}) #silent $prepare_json($f.formatChoice.GTF, extra_data_dict) #end if #if $f.formatChoice.format_select == 'bigwig' --bigwig $f.formatChoice.BIGWIG + #set pos_color = str($f.formatChoice.pos_color) + #set neg_color = str($f.formatChoice.neg_color) + #silent $extra_data_dict.update({"pos_color" : $pos_color, "neg_color" : $neg_color}) #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict) #end if #end for @@ -111,13 +116,6 @@ label="BAM File" /> <param name="label" type="text" size="30" value = "Sequence 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="bed"> <conditional name="bedChoice"> @@ -159,10 +157,6 @@ label="Blast Alignments File" /> <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" /> - <param name="track_type" type="select" label="Set trackType"> - <option value="CanvasFeatures">CanvasFeatures (Default)</option> - <option value="G-OnRamp_plugin/BlastAlignment">BlastAlignment (contain advanced features, need install G_OnRamp_plugin</option> - </param> <param name="track_color" type="color" label="Track color" value="#daa520"> <sanitizer> <valid initial="string.letters,string.digits"> @@ -179,7 +173,14 @@ label="BIGWIG File" /> <param name="label" type="text" size="30" value="Sequence Coverage" label="Track name" /> - <param name="track_color" type="color" label="Track color" value="#daa520"> + <param name="pos_color" type="color" label="Positive Coverage Color" value="#FFA600"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + <param name="neg_color" type="color" label="Negative Coverage Color" value="#005EFF"> <sanitizer> <valid initial="string.letters,string.digits"> <add value="#"/> @@ -211,10 +212,6 @@ </when> </conditional> <param name="label" type="text" size="30" value="Gene Prediction" label="Track name" /> - <param name="track_type" type="select" label="Set trackType"> - <option value="CanvasFeatures">CanvasFeatures (Default)</option> - <option value="G-OnRamp_plugin/GenePred">GenePred (contain advanced features, need install G_OnRamp_plugin</option> - </param> <param name="track_color" type="color" label="Track color" value="#daa520"> <sanitizer> <valid initial="string.letters,string.digits">
--- a/trackObject.py Fri Mar 17 16:28:21 2017 -0400 +++ b/trackObject.py Fri Mar 17 19:00:01 2017 -0400 @@ -60,14 +60,22 @@ utils.gtfToGff3(dataFile, des_path, self.chrom_size) track['fileName'] = fileName track['dataType'] = dataType + self.SetMetadata(track, metaData) + self.tracks.append(track) + + #If the metadata is not set, use the default value + def SetMetadata(self, track, metaData): track.update(metaData) - #If the metadata is not set, use the default value if 'name' not in metaData.keys() or track['name'] == '': - track['name'] = fileName + track['name'] = track['fileName'] if 'label' not in metaData.keys() or track['label'] == '': track['label'] = track['name'] if 'track_color' not in metaData.keys() or track['track_color'] == '': track['track_color'] = "#daa520" if 'track_type' not in metaData.keys() or track['track_type'] == '': track['track_type'] = "CanvasFeatures" - self.tracks.append(track) + if track['dataType'] == 'bigwig': + if 'pos_color' not in metaData.keys() or track['pos_color'] == '': + track['pos_color'] = "#FFA600" + if 'neg_color' not in metaData.keys() or track['neg_color'] == '': + track['neg_color'] = "#005EFF"