Mercurial > repos > yating-l > hubarchivecreator

changeset 6:2cc7685a7182 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 48b59e91e2dcc2e97735ee35d587960cbfbce932
author yating-l
date Wed, 21 Dec 2016 18:00:09 -0500
parents 7b0d359de7ee
children dd1e233e16a1
files Bam.pyc Bed.pyc BedSimpleRepeats.pyc BedSpliceJunctions.py BedSpliceJunctions.pyc BigWig.pyc Datatype.pyc Dbia3.chrom.size Gff3.pyc Gtf.pyc Psl.pyc Track.pyc TrackDb.pyc TrackHub.pyc hubArchiveCreator.py hubArchiveCreator.xml out spliceJunctions.as test-data/bed_splice_junctions/__main__.log test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed util/Fasta.pyc util/Filters.pyc util/__init__.pyc util/subtools.pyc
diffstat 22 files changed, 154 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
Binary file Bam.pyc has changed
Binary file Bed.pyc has changed
Binary file BedSimpleRepeats.pyc has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BedSpliceJunctions.py	Wed Dec 21 18:00:09 2016 -0500
@@ -0,0 +1,70 @@
+#!/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))
Binary file BedSpliceJunctions.pyc has changed
Binary file BigWig.pyc has changed
Binary file Datatype.pyc has changed
Binary file Gff3.pyc has changed
Binary file Gtf.pyc has changed
Binary file Psl.pyc has changed
Binary file Track.pyc has changed
Binary file TrackDb.pyc has changed
Binary file TrackHub.pyc has changed
--- a/hubArchiveCreator.py	Wed Dec 21 17:26:51 2016 -0500
+++ b/hubArchiveCreator.py	Wed Dec 21 18:00:09 2016 -0500
@@ -18,6 +18,7 @@
 # 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
@@ -46,6 +47,9 @@
     # 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')
 
@@ -113,6 +117,7 @@
     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
@@ -139,6 +144,7 @@
                         (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)]:
--- a/hubArchiveCreator.xml	Wed Dec 21 17:26:51 2016 -0500
+++ b/hubArchiveCreator.xml	Wed Dec 21 18:00:09 2016 -0500
@@ -111,6 +111,11 @@
                         #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
@@ -206,6 +211,7 @@
                             <param name="bed_select" type="select" label="Bed Choice">
                                 <option value="bed_generic" selected="true">BED Generic (bed3+)</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>
                             </param>
                             <when value="bed_generic">
                                 <param
@@ -224,6 +230,14 @@
                                         label="Bed Simple Repeats (Bed4+12) File"
                                 />
                             </when>
+                            <when value="bed_splice_junctions_option">
+                                <param
+                                        format="bed"
+                                        name="BED_splice_junctions"
+                                        type="data"
+                                        label="Bed Splice Junctions (Bed12+1) File"
+                                />
+                            </when>
                         </conditional>
                         <param name="track_color" type="color" label="Track color" value="#000000">
                             <sanitizer>
@@ -442,6 +456,7 @@
                 />
             </output>
         </test>
+        
 
         <!-- Test with Psl -->
         <test>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spliceJunctions.as	Wed Dec 21 18:00:09 2016 -0500
@@ -0,0 +1,17 @@
+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"
+    )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_splice_junctions/__main__.log	Wed Dec 21 18:00:09 2016 -0500
@@ -0,0 +1,6 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed	Wed Dec 21 18:00:09 2016 -0500
@@ -0,0 +1,40 @@
+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
+contig16	12796	21322	JUNC00000013	1000	-	12796	21322	255,0,0	2	15,75	0,8451	1
+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
Binary file util/Fasta.pyc has changed
Binary file util/Filters.pyc has changed
Binary file util/__init__.pyc has changed
Binary file util/subtools.pyc has changed