# HG changeset patch
# User yating-l
# Date 1482359211 18000
# Node ID 7b0d359de7ee5e4f28562d88b46194765e693950
# Parent 9018229c0969f81eb8effb698be79dd435fffcb2
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e2db8aa3672f1222b415716054bfb3c5ccd132a1-dirty
diff -r 9018229c0969 -r 7b0d359de7ee Bam.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee Bed.pyc
Binary file Bed.pyc has changed
diff -r 9018229c0969 -r 7b0d359de7ee BedSimpleRepeats.pyc
Binary file BedSimpleRepeats.pyc has changed
diff -r 9018229c0969 -r 7b0d359de7ee BedSpliceJunctions.py
--- a/BedSpliceJunctions.py Wed Dec 21 12:09:58 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-#!/usr/bin/python
-
-import os
-import tempfile
-
-from Datatype import Datatype
-from Track import Track
-from TrackDb import TrackDb
-from util import subtools
-
-
-class BedSpliceJunctions( Datatype ):
- def __init__(self, input_bed_splice_junctions_false_path, data_bed_splice_junctions):
-
- super(BedSpliceJunctions, self).__init__()
-
- self.input_bed_splice_junctions_false_path = input_bed_splice_junctions_false_path
- self.name_bed_splice_junctions = data_bed_splice_junctions["name"]
- self.priority = data_bed_splice_junctions["order_index"]
- self.track_color = data_bed_splice_junctions["track_color"]
- # TODO: Think about how to avoid repetition of the group_name everywhere
- self.group_name = data_bed_splice_junctions["group_name"]
-
- sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
-
- # Sort processing
- subtools.sort(self.input_bed_splice_junctions_false_path, sortedBedFile.name)
-
- # bedToBigBed processing
- # TODO: Change the name of the bb, to tool + genome + .bb
- trackName = "".join( ( self.name_bed_splice_junctions, '.bb' ) )
- myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
-
- auto_sql_option = os.path.join(self.tool_directory, 'spliceJunctions.as')
-
- with open(myBigBedFilePath, 'w') as bigBedFile:
- subtools.bedToBigBed(sortedBedFile.name,
- self.chromSizesFile.name,
- bigBedFile.name,
- typeOption='bed12+1',
- autoSql=auto_sql_option)
-
- # Create the Track Object
- self.createTrack(file_path=trackName,
- track_name=trackName,
- long_label=self.name_bed_splice_junctions, track_type='bigBed 12 +', visibility='dense',
- 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_splice_junctions)
- #print("- %s created in %s" % (trackName, myBigBedFilePath))
diff -r 9018229c0969 -r 7b0d359de7ee BedSpliceJunctions.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee BigWig.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee Datatype.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee Gff3.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee Gtf.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee Psl.pyc
Binary file Psl.pyc has changed
diff -r 9018229c0969 -r 7b0d359de7ee Track.pyc
Binary file Track.pyc has changed
diff -r 9018229c0969 -r 7b0d359de7ee TrackDb.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee TrackHub.pyc
Binary file TrackHub.pyc has changed
diff -r 9018229c0969 -r 7b0d359de7ee hubArchiveCreator.py
--- a/hubArchiveCreator.py Wed Dec 21 12:09:58 2016 -0500
+++ b/hubArchiveCreator.py Wed Dec 21 17:26:51 2016 -0500
@@ -18,7 +18,6 @@
# Internal dependencies
from Bam import Bam
from BedSimpleRepeats import BedSimpleRepeats
-from BedSpliceJunctions import BedSpliceJunctions
from Bed import Bed
from BigWig import BigWig
from util.Fasta import Fasta
@@ -47,9 +46,6 @@
# Bed4+12 (TrfBig)
parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
- # Bed12+1 (regtools)
- parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')
-
# Generic Bed (Blastx transformed to bed)
parser.add_argument('--bed', action='append', help='Bed generic format')
@@ -117,7 +113,6 @@
array_inputs_bam = args.bam
array_inputs_bed_generic = args.bed
array_inputs_bed_simple_repeats = args.bedSimpleRepeats
- array_inputs_bed_splice_junctions = args.bedSpliceJunctions
array_inputs_bigwig = args.bigwig
array_inputs_gff3 = args.gff3
array_inputs_gtf = args.gtf
@@ -144,7 +139,6 @@
(array_inputs_bed_generic, Bed),
(array_inputs_bigwig, BigWig),
(array_inputs_bed_simple_repeats, BedSimpleRepeats),
- (array_inputs_bed_splice_junctions, BedSpliceJunctions),
(array_inputs_gff3, Gff3),
(array_inputs_gtf, Gtf),
(array_inputs_psl, Psl)]:
diff -r 9018229c0969 -r 7b0d359de7ee hubArchiveCreator.xml
--- a/hubArchiveCreator.xml Wed Dec 21 12:09:58 2016 -0500
+++ b/hubArchiveCreator.xml Wed Dec 21 17:26:51 2016 -0500
@@ -111,11 +111,6 @@
#silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
extra_data_dict)
#end if
- #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
- --bedSpliceJunctions $f.formatChoice.bedChoice.Bed_splice_junctions
- #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
- extra_data_dict)
- #end if
#end if
#if $f.formatChoice.format_select == "psl"
--psl $f.formatChoice.PSL
@@ -211,7 +206,6 @@
-
-
-
-
@@ -456,7 +442,6 @@
/>
-
diff -r 9018229c0969 -r 7b0d359de7ee spliceJunctions.as
--- a/spliceJunctions.as Wed Dec 21 12:09:58 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-table spliceJunctions
-"Predicted splice junctions"
- (
- string chrom; "Reference sequence chromosome or scaffold"
- uint chromStart; "Start position in chromosome"
- uint chromEnd; "End position in chromosome"
- string name; "Name of item"
- uint score; "Score from 0-1000"
- char[1] strand; "+ or -"
- uint thickStart; "Start of where display should be thick (start codon)"
- uint thickEnd; "End of where display should be thick (stop codon)"
- uint reserved; "Used as itemRgb as of 2004-11-22"
- int blockCount; "Number of blocks"
- int[blockCount] blockSizes; "Comma separated list of block sizes"
- int[blockCount] chromStarts; "Start positions relative to chromStart"
- uint junctionScore; "Number of reads supporting the splice junction"
- )
diff -r 9018229c0969 -r 7b0d359de7ee test-data/bed_splice_junctions/__main__.log
--- a/test-data/bed_splice_junctions/__main__.log Wed Dec 21 12:09:58 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
-
-DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
-
-DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
-
diff -r 9018229c0969 -r 7b0d359de7ee test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed
--- a/test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed Wed Dec 21 12:09:58 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-contig16 1808 11364 JUNC00000001 1000 - 1808 11364 255,0,0 2 89,80 0,9476 17
-contig16 11374 11605 JUNC00000003 1000 - 11374 11605 255,0,0 2 89,88 0,143 18
-contig16 11617 11783 JUNC00000004 1000 - 11617 11783 255,0,0 2 65,25 0,141 1
-contig16 11617 11844 JUNC00000005 1000 - 11617 11844 255,0,0 2 88,86 0,141 22
-contig16 11774 11977 JUNC00000006 1000 - 11774 11977 255,0,0 2 84,56 0,147 13
-contig16 11806 11956 JUNC00000007 1000 - 11806 11956 255,0,0 2 55,35 0,115 1
-contig16 11921 12673 JUNC00000008 1000 - 11921 12673 255,0,0 2 54,73 0,679 13
-contig16 11939 17275 JUNC00000009 1000 - 11939 17275 255,0,0 2 36,54 0,5282 1
-contig16 12723 17294 JUNC00000011 1000 - 12723 17294 255,0,0 2 88,73 0,4498 11
-contig16 12782 21003 JUNC00000012 1000 - 12782 21003 255,0,0 2 29,61 0,8160 1
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-contig16 17251 17490 JUNC00000014 1000 - 17251 17490 255,0,0 2 86,85 0,154 17
-contig16 17307 21307 JUNC00000015 1000 - 17307 21307 255,0,0 2 30,60 0,3940 1
-contig16 21007 21283 JUNC00000016 1000 - 21007 21283 255,0,0 2 54,36 0,240 1
-contig16 21250 22512 JUNC00000017 1000 - 21250 22512 255,0,0 2 86,58 0,1204 8
-contig16 21316 23083 JUNC00000018 1000 - 21316 23083 255,0,0 2 20,70 0,1697 1
-contig16 22206 25356 JUNC00000019 1000 + 22206 25356 255,0,0 2 39,46 0,3104 1
-contig16 27016 27178 JUNC00000021 1000 + 27016 27178 255,0,0 2 33,70 0,92 2
-contig16 27196 34369 JUNC00000022 1000 + 27196 34369 255,0,0 2 57,32 0,7141 1
-contig16 29103 29238 JUNC00000023 1000 + 29103 29238 255,0,0 2 61,18 0,117 1
-contig16 29358 34416 JUNC00000024 1000 + 29358 34416 255,0,0 2 11,79 0,4979 1
-contig16 34568 34768 JUNC00000025 1000 + 34568 34768 255,0,0 2 51,84 0,116 3
-contig16 34573 34763 JUNC00000026 1000 + 34573 34763 255,0,0 2 46,44 0,146 1
-contig16 34782 34954 JUNC00000027 1000 + 34782 34954 255,0,0 2 53,66 0,106 4
-contig16 35110 42519 JUNC00000028 1000 + 35110 42519 255,0,0 2 64,64 0,7345 4
-contig16 42508 43097 JUNC00000030 1000 + 42508 43097 255,0,0 2 82,65 0,524 6
-contig16 43273 43505 JUNC00000031 1000 + 43273 43505 255,0,0 2 81,85 0,147 12
-contig17 1242 2504 JUNC00000032 1000 - 1242 2504 255,0,0 2 86,58 0,1204 8
-contig17 1308 3075 JUNC00000033 1000 - 1308 3075 255,0,0 2 20,70 0,1697 1
-contig17 2198 5348 JUNC00000034 1000 + 2198 5348 255,0,0 2 39,46 0,3104 1
-contig17 7008 7170 JUNC00000036 1000 + 7008 7170 255,0,0 2 33,70 0,92 2
-contig17 7188 14361 JUNC00000037 1000 + 7188 14361 255,0,0 2 57,32 0,7141 1
-contig17 9095 9230 JUNC00000038 1000 + 9095 9230 255,0,0 2 61,18 0,117 1
-contig17 9350 14408 JUNC00000039 1000 + 9350 14408 255,0,0 2 11,79 0,4979 1
-contig17 14560 14760 JUNC00000040 1000 + 14560 14760 255,0,0 2 51,84 0,116 3
-contig17 14565 14755 JUNC00000041 1000 + 14565 14755 255,0,0 2 46,44 0,146 1
-contig17 14774 14946 JUNC00000042 1000 + 14774 14946 255,0,0 2 53,66 0,106 4
-contig17 15102 22511 JUNC00000043 1000 + 15102 22511 255,0,0 2 64,64 0,7345 4
-contig17 22500 23089 JUNC00000045 1000 + 22500 23089 255,0,0 2 82,65 0,524 6
-contig17 23265 23497 JUNC00000046 1000 + 23265 23497 255,0,0 2 81,85 0,147 12
diff -r 9018229c0969 -r 7b0d359de7ee util/Fasta.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee util/Filters.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee util/__init__.pyc
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diff -r 9018229c0969 -r 7b0d359de7ee util/subtools.pyc
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