# HG changeset patch
# User yating-l
# Date 1482337107 18000
# Node ID 44577d6784b730cee5bcb0e781db9bb3936d14f6
# Parent  4ced8f116509f8d88b32a2ef48d705d3415100b3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e2db8aa3672f1222b415716054bfb3c5ccd132a1-dirty

diff -r 4ced8f116509 -r 44577d6784b7 Bam.py
diff -r 4ced8f116509 -r 44577d6784b7 Bam.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 Bed.py
diff -r 4ced8f116509 -r 44577d6784b7 Bed.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 BedSimpleRepeats.py
diff -r 4ced8f116509 -r 44577d6784b7 BedSimpleRepeats.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 BedSpliceJunctions.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BedSpliceJunctions.py	Wed Dec 21 11:18:27 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))
diff -r 4ced8f116509 -r 44577d6784b7 BedSpliceJunctions.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 BigWig.py
diff -r 4ced8f116509 -r 44577d6784b7 BigWig.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 Datatype.py
diff -r 4ced8f116509 -r 44577d6784b7 Datatype.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 Gff3.py
diff -r 4ced8f116509 -r 44577d6784b7 Gff3.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 Gtf.py
diff -r 4ced8f116509 -r 44577d6784b7 Gtf.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 LICENSE.txt
diff -r 4ced8f116509 -r 44577d6784b7 Psl.py
diff -r 4ced8f116509 -r 44577d6784b7 Psl.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 Track.py
diff -r 4ced8f116509 -r 44577d6784b7 Track.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 TrackDb.py
diff -r 4ced8f116509 -r 44577d6784b7 TrackDb.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 TrackHub.py
diff -r 4ced8f116509 -r 44577d6784b7 TrackHub.pyc
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diff -r 4ced8f116509 -r 44577d6784b7 __init__.py
diff -r 4ced8f116509 -r 44577d6784b7 bigGenePred.as
diff -r 4ced8f116509 -r 44577d6784b7 bigPsl.as
diff -r 4ced8f116509 -r 44577d6784b7 doc/Makefile
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/.buildinfo
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/.doctrees/doc/index.doctree
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/.doctrees/environment.pickle
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/.doctrees/index.doctree
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diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/.buildinfo
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/_modules/hubArchiveCreator.html
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/_modules/index.html
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diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/_static/pygments.css
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/_static/searchtools.js
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/_static/sidebar.js
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/_static/underscore-1.3.1.js
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/_static/underscore.js
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diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/_static/websupport.js
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/code.html
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/genindex.html
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/index.html
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/objects.inv
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/py-modindex.html
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/search.html
diff -r 4ced8f116509 -r 44577d6784b7 doc/_build/html/searchindex.js
diff -r 4ced8f116509 -r 44577d6784b7 doc/code.rst
diff -r 4ced8f116509 -r 44577d6784b7 doc/conf.py
diff -r 4ced8f116509 -r 44577d6784b7 doc/index.rst
diff -r 4ced8f116509 -r 44577d6784b7 doc/make.bat
diff -r 4ced8f116509 -r 44577d6784b7 hubArchiveCreator.py
--- a/hubArchiveCreator.py	Tue Nov 22 17:13:18 2016 -0500
+++ b/hubArchiveCreator.py	Wed Dec 21 11:18:27 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)]:
diff -r 4ced8f116509 -r 44577d6784b7 hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Tue Nov 22 17:13:18 2016 -0500
+++ b/hubArchiveCreator.xml	Wed Dec 21 11:18:27 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>
diff -r 4ced8f116509 -r 44577d6784b7 spliceJunctions.as
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spliceJunctions.as	Wed Dec 21 11:18:27 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"
+    )
diff -r 4ced8f116509 -r 44577d6784b7 templates/__init__.py
diff -r 4ced8f116509 -r 44577d6784b7 templates/display.txt
diff -r 4ced8f116509 -r 44577d6784b7 templates/genomesAssembly/__init__.py
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diff -r 4ced8f116509 -r 44577d6784b7 templates/groupsTxt/__init__.py
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diff -r 4ced8f116509 -r 44577d6784b7 templates/hubDescription/__init__.py
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diff -r 4ced8f116509 -r 44577d6784b7 templates/hubTxt/__init__.py
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diff -r 4ced8f116509 -r 44577d6784b7 templates/specieDescription/__init__.py
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diff -r 4ced8f116509 -r 44577d6784b7 templates/trackDb/__init__.py
diff -r 4ced8f116509 -r 44577d6784b7 templates/trackDb/layout.txt
diff -r 4ced8f116509 -r 44577d6784b7 test-data/all_datatypes/__main__.log
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diff -r 4ced8f116509 -r 44577d6784b7 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam
diff -r 4ced8f116509 -r 44577d6784b7 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai
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diff -r 4ced8f116509 -r 44577d6784b7 test-data/all_datatypes/myHub/genomes.txt
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diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/__main__.log
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/bed_simple_repeats_trackhub.html
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/myHub/Dbia3.html
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diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/myHub/Dbia3/description.html
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/myHub/Dbia3/groups.txt
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/myHub/Dbia3/trackDb.txt
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/myHub/genomes.txt
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_simple_repeats/myHub/hub.txt
diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed
--- /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 11:18:27 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
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diff -r 4ced8f116509 -r 44577d6784b7 test-data/bed_splice_junctions/myHub/__main__.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_splice_junctions/myHub/__main__.log	Wed Dec 21 11:18:27 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 ####
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diff -r 4ced8f116509 -r 44577d6784b7 test-data/two_groups_one_track_first/myHub/Dbia3/description.html
diff -r 4ced8f116509 -r 44577d6784b7 test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt
diff -r 4ced8f116509 -r 44577d6784b7 test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt
diff -r 4ced8f116509 -r 44577d6784b7 test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig
diff -r 4ced8f116509 -r 44577d6784b7 test-data/two_groups_one_track_first/myHub/genomes.txt
diff -r 4ced8f116509 -r 44577d6784b7 test-data/two_groups_one_track_first/myHub/hub.txt
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diff -r 4ced8f116509 -r 44577d6784b7 todo.md
--- a/todo.md	Tue Nov 22 17:13:18 2016 -0500
+++ b/todo.md	Wed Dec 21 11:18:27 2016 -0500
@@ -1,37 +1,3 @@
-### TEMP St Louis ###
-- How to manage messages to user and debugging:
-    - User should receive INFO / WARN / ERROR / CRITICAL:
-        - User summary informations in stdout
-        - Full error in stderr
-    - Developer should receive all Logging stack:
-        - Not the user summary in stdout
-        - Full stack in stdout and stderr directly
-
-    - HOWTO:
-        - Manage (at least) two type of Logging types:
-            - The user one => When Debug mode is not set or disabled
-            - The dev one => When Debug mode is enabled
-        - User:
-            - Two Handlers: stdout and stderr
-            - STDOUT:
-                - Filter stdout:
-                    - NO ERROR and CRITICAL here
-                    - (Warn)
-                - Formatter:
-                    - Only show %(message) for clarity
-            - STDERR:
-                - Filter stderr => WARN / ERRROR / CRITICAL
-                - Formatter:
-                    - Show message
-                    - Show traceback
-        - Dev:
-            - One Handler:
-                - To both stdout and stderr
-            - Filter:
-                - Nope?
-            - Formatter:
-                - Show traceback in both
-
 # HubArchiveCreator's TODO
 
 *TODO file inspired from: http://lifehacker.com/why-a-github-gist-is-my-favorite-to-do-list-1493063613*
@@ -39,29 +5,30 @@
 ### TO COMPLETE
 
 
+- [ ] Parse the [JSON received from Galaxy inputs](hubArchiveCreator.xml#L47-L137) in a class instead of doing [this spaghetti code](hubArchiveCreator.py#L137-L149)
 - [ ] Don't let the Tool Classes manage the archive (add or remove files / folders) => Everything should pass through TrackHub or another class dedicated to that
 - [ ] Move the class and others program related files, into separated folders
 - [ ] Take into account the name of the reference genome / the change:
   - [ ] Somebody could want to launch two visualisations of two different genomes. Repeats of Genome with extensions associated
-- [ ] Add TDD => First add the test. It should not pass. Implement. It should now pass :)
-- [ ] Replace Gff3 by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat
-- [ ] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm)
+- [ ] Replace Gff3/GTF by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat
 - [ ] Manage the error when a user is selecting Generic Bed instead of Bed Simple Repeats. Two options: a. Output a better error message ("Check with the other Bed options") b. Identify internally this is not a regular BED but a specific one
 - [ ] Remove the non-explicit parameters for the communication between Galaxy Wrapper and the entry point
-- [ ] Rename all occurences of `extension` which `datatype`
+- [ ] Rename all occurences of `extension` with `datatype`
 - [ ] Follow https://google.github.io/styleguide/pyguide.html
-- [ ] Move to Python 3
-- [ ] Remove the repetition of the extension if it already exists
+- [ ] Migrate to Python 3
+- [ ] Remove the repetition of the extension file if it already exists
 - [ ] Better thinking about the tool_directory management / Classes path refactoring
-- [ ] Add a debug mode to have more outputs
-- [ ] Improve the standard output of HAC
-- [ ] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml
-- [ ] Sort the order of the HTML directories/files
 
 ### DONE
 
 
+- [x] Add TDD => First add the test. It should not pass. Implement. It should now pass :)
+- [x] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm)
+- [x] Add a debug mode to have more outputs
+- [x] Improve the standard output of HAC
 - [x] Each time a file is added => Print it in the output with the full path (or relative path to root)
+- [x] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml
+- [x] Sort the order of the HTML directories/files
 - [x] Add a script for Linux.x86_64 to download and and chmod +x the dependencies for local testing => util/install_linux_binaries.py
 - [x] Add sorting BED if not sorted (Use the output of bedToBigBed)
 - [x] Add a script to install the huba datatype
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