Mercurial > repos > yating-l > hubarchivecreator
changeset 54:4a58094b051e draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
| author | yating-l |
|---|---|
| date | Tue, 16 May 2017 18:09:00 -0400 |
| parents | 44059c9e7c02 |
| children | ba9997c847dc |
| files | cytoBand.py cytoBandIdeo.as hubArchiveCreator.py hubArchiveCreator.xml |
| diffstat | 4 files changed, 103 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cytoBand.py Tue May 16 18:09:00 2017 -0400 @@ -0,0 +1,74 @@ +#!/usr/bin/python + +import os +import tempfile + +from Datatype import Datatype +from Track import Track +from TrackDb import TrackDb +from util import subtools + + +class cytoBand( Datatype ): + def __init__(self, input_bed_cytoBand_false_path, data_bed_cytoBand): + + super(cytoBand, self).__init__() + + self.input_bed_cytoBand_false_path = input_bed_cytoBand_false_path + self.name_bed_cytoBand = data_bed_cytoBand["name"] + self.priority = data_bed_cytoBand["order_index"] + self.track_color = data_bed_cytoBand["track_color"] + # TODO: Think about how to avoid repetition of the group_name everywhere + self.group_name = data_bed_cytoBand["group_name"] + if data_bed_cytoBand["long_label"]: + self.long_label = data_bed_cytoBand["long_label"] + else: + self.long_label = self.name_bed_cytoBand + sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") + + # Sort processing + subtools.sort(self.input_bed_cytoBand_false_path, sortedBedFile.name) + + # bedToBigBed processing + # TODO: Change the name of the bb, to tool + genome + .bb + trackName = "".join( ( self.name_bed_cytoBand, '.bb' ) ) + myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) + + auto_sql_option = os.path.join(self.tool_directory, 'cytoBandIdeo.as') + + with open(myBigBedFilePath, 'w') as bigBedFile: + subtools.bedToBigBed(sortedBedFile.name, + self.chromSizesFile.name, + bigBedFile.name, + typeOption='bed4', + autoSql=auto_sql_option) + + # Create the Track Object + self.createTrack(file_path=trackName, + track_name='cytoBandIdeo', + long_label=self.long_label, + track_type='bigBed', + priority=self.priority, + track_file=myBigBedFilePath, + track_color=self.track_color, + group_name=self.group_name) + + # dataURL = "tracks/%s" % trackName + # + # trackDb = TrackDb( + # trackName=trackName, + # longLabel=self.name_bed_simple_repeats, + # shortLabel=self.getShortName( self.name_bed_simple_repeats ), + # trackDataURL=dataURL, + # trackType='bigBed 4 +', + # visibility='dense', + # priority=self.priority, + # ) + # + # self.track = Track( + # trackFile=myBigBedFilePath, + # trackDb=trackDb, + # ) + + print("- Bed splice junctions %s created" % self.name_bed_cytoBand) + #print("- %s created in %s" % (trackName, myBigBedFilePath))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cytoBandIdeo.as Tue May 16 18:09:00 2017 -0400 @@ -0,0 +1,9 @@ +table cytoBandIdeo +"cytoBandIdeo Describes the positions of cytogenetic bands with a chromosome" + ( + string chrom; "Reference sequence chromosome or scaffold" + uint chromStart; "Start position in chromosome" + uint chromEnd; "End position in chromosome" + string name; "Name of item" + string gieStain; "Giemsa stain results: gneg gpos25 gpos50 gpos75 gpos100 acen gvar stalk" + ) \ No newline at end of file
--- a/hubArchiveCreator.py Thu May 11 17:27:15 2017 -0400 +++ b/hubArchiveCreator.py Tue May 16 18:09:00 2017 -0400 @@ -20,6 +20,7 @@ from BedSimpleRepeats import BedSimpleRepeats from BedSpliceJunctions import BedSpliceJunctions from Bed import Bed +from cytoBand import cytoBand from BigWig import BigWig from util.Fasta import Fasta from util.Filters import TraceBackFormatter @@ -55,6 +56,9 @@ # Generic Bed (Blastx transformed to bed) parser.add_argument('--bed', action='append', help='Bed generic format') + #cytoBandIdeo + parser.add_argument('--cytoBand', action='append', help='Cytoband Track, using cytoBandIdeo.as') + # BigPsl (blat alignment) parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as') @@ -124,6 +128,7 @@ # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH} array_inputs_bam = args.bam array_inputs_bed_generic = args.bed + array_inputs_bed_cytoBand = args.cytoBand array_inputs_bed_simple_repeats = args.bedSimpleRepeats array_inputs_bed_splice_junctions = args.bedSpliceJunctions array_inputs_bigwig = args.bigwig @@ -152,6 +157,7 @@ for (inputs, datatype_class) in [ (array_inputs_bam, Bam), (array_inputs_bed_generic, Bed), + (array_inputs_bed_cytoBand, cytoBand), (array_inputs_bigwig, BigWig), (array_inputs_bed_simple_repeats, BedSimpleRepeats), (array_inputs_bed_splice_junctions, BedSpliceJunctions),
--- a/hubArchiveCreator.xml Thu May 11 17:27:15 2017 -0400 +++ b/hubArchiveCreator.xml Tue May 16 18:09:00 2017 -0400 @@ -91,6 +91,11 @@ #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, extra_data_dict) #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand" + --cytoBand $f.formatChoice.bedChoice.BED_cytoBand + #silent $prepare_json($f.formatChoice.bedChoice.BED_cytoBand, $index_track_final, + extra_data_dict) + #end if #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, $index_track_final, @@ -206,6 +211,7 @@ <conditional name="bedChoice"> <param name="bed_select" type="select" label="Bed Choice"> <option value="bed_generic" selected="true">BED Generic (bed3+)</option> + <option value="bed_cytoBand">cytoBand Track (bed4)</option> <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option> @@ -220,6 +226,14 @@ /> </when> + <when value="bed_cytoBand"> + <param + format="bed" + name="BED_cytoBand" + type="data" + label="cytoBand Track (Bed4)" + /> + </when> <when value="bed_simple_repeats_option"> <param format="bed"