# HG changeset patch
# User yating-l
# Date 1496244916 14400
# Node ID fcc1021bd49607d3bc219b19636ee0f4e15ec7b0
# Parent  2677f1899aa861849c1a210e1474e01c41d14597
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty

diff -r 2677f1899aa8 -r fcc1021bd496 Bam.pyc
Binary file Bam.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 Bed.pyc
Binary file Bed.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 BedBlastAlignments.pyc
Binary file BedBlastAlignments.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 BedSimpleRepeats.pyc
Binary file BedSimpleRepeats.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 BedSpliceJunctions.pyc
Binary file BedSpliceJunctions.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 BigBed.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BigBed.py	Wed May 31 11:35:16 2017 -0400
@@ -0,0 +1,79 @@
+#!/usr/bin/python
+
+import os
+import shutil
+from subprocess import Popen, PIPE
+import re
+
+# Internal dependencies
+from Datatype import Datatype
+
+class BigBed(Datatype):
+    """ Configurations for creating the bigBed evidence track """
+
+    def __init__(self, input_bigbed_path, data_bigbed):
+        super(BigBed, self).__init__()
+
+        self.track = None
+
+        self.input_bigbed_path = input_bigbed_path
+        self.name_bigbed = data_bigbed["name"]
+        self.priority = data_bigbed["order_index"]
+        self.track_color = data_bigbed["track_color"]
+        self.group_name = data_bigbed["group_name"]
+
+        track_name = "".join((self.name_bigbed, ".bigbed"))
+        if data_bigbed["long_label"]:
+            self.long_label = data_bigbed["long_label"]
+        else:
+            self.long_label = self.name_bigbed
+
+        bigbed_file_path = os.path.join(self.myTrackFolderPath, track_name)
+
+        track_type = self.determine_track_type(input_bigbed_path)
+
+        shutil.copy(self.input_bigbed_path, bigbed_file_path)
+
+        # Create the Track Object
+        self.createTrack(file_path=track_name,
+                         track_name=track_name,
+                         long_label=self.long_label,
+                         track_type=track_type,
+                         visibility='hide',
+                         priority=self.priority,
+                         track_file=bigbed_file_path,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        print "- BigBed %s created" % self.name_bigbed
+
+
+    def determine_track_type(self, bb_file):
+        """
+        Determine the number of standard and extra fields using bigBedSummary
+
+        Implementation of reading from stdout is based on a Stackoverflow post:
+        http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate
+
+        :param bb_file: path to a bigBed file
+
+        :returns: the bigBed track type
+        """
+
+        cmd_ph = Popen(["bigBedSummary", "-fields", bb_file, "stdout"],
+                       stdout=PIPE, bufsize=1)
+
+        pattern = r"(\d+) bed definition fields, (\d+) total fields"
+
+        with cmd_ph.stdout:
+            for line in iter(cmd_ph.stdout.readline, b''):
+                match = re.match(pattern, line)
+
+                if match:
+                    extra_mark = "." if match.group(1) == match.group(2) else "+"
+                    bed_type = "bigBed %s %s" % (match.group(1), extra_mark)
+                    break
+
+        cmd_ph.wait()
+
+        return bed_type
diff -r 2677f1899aa8 -r fcc1021bd496 BigWig.py
--- a/BigWig.py	Tue May 09 15:42:43 2017 -0400
+++ b/BigWig.py	Wed May 31 11:35:16 2017 -0400
@@ -2,6 +2,8 @@
 
 import os
 import shutil
+from subprocess import Popen, PIPE
+import re
 
 # Internal dependencies
 from Datatype import Datatype
@@ -36,30 +38,37 @@
         self.createTrack(file_path=trackName,
                          track_name=trackName,
                          long_label=self.long_label,
-                         track_type='bigWig', visibility='full',
+                         track_type=self.determine_track_type(myBigWigFilePath),
+                         visibility='full',
                          priority=self.priority,
                          track_file=myBigWigFilePath,
                          track_color=self.track_color,
                          group_name=self.group_name)
 
-        # dataURL = "tracks/%s" % trackName
-        #
-        # # Return the BigBed track
-        #
-        # trackDb = TrackDb(
-        #     trackName=trackName,
-        #     longLabel=self.name_bigwig,
-        #     shortLabel=self.getShortName( self.name_bigwig ),
-        #     trackDataURL=dataURL,
-        #     trackType='bigWig',
-        #     visibility='full',
-        #     priority=self.priority,
-        # )
-        #
-        # self.track = Track(
-        #     trackFile=myBigWigFilePath,
-        #     trackDb=trackDb,
-        # )
-
         print("- BigWig %s created" % self.name_bigwig)
         #print("- %s created in %s" % (trackName, myBigWigFilePath))
+
+    def determine_track_type(self, bw_file):
+        """
+        bigWig tracks must declare the expected signal range for the data
+        (See https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html).
+        This method determines the range of values for a bigWig file using
+        the bigWigInfo program.
+
+        Implementation of reading from stdout is based on a Stackoverflow post:
+        http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate
+
+        :param bw_file: path to a bigWig file
+
+        :returns: the bigWig track type
+        """
+        cmd_ph = Popen(["bigWigInfo", "-minMax", bw_file],
+                       stdout=PIPE, bufsize=1)
+
+        with cmd_ph.stdout:
+            for line in iter(cmd_ph.stdout.readline, b''):
+                bw_type = "bigWig %s" % line.rstrip()
+
+        cmd_ph.wait()
+
+        return bw_type
diff -r 2677f1899aa8 -r fcc1021bd496 BigWig.pyc
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diff -r 2677f1899aa8 -r fcc1021bd496 Datatype.pyc
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diff -r 2677f1899aa8 -r fcc1021bd496 Gff3.pyc
Binary file Gff3.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 Gtf.pyc
Binary file Gtf.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 Psl.pyc
Binary file Psl.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 bigPsl.pyc
Binary file bigPsl.pyc has changed
diff -r 2677f1899aa8 -r fcc1021bd496 cytoBand.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cytoBand.py	Wed May 31 11:35:16 2017 -0400
@@ -0,0 +1,75 @@
+#!/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',
+                         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_cytoBand)
+        #print("- %s created in %s" % (trackName, myBigBedFilePath))
diff -r 2677f1899aa8 -r fcc1021bd496 cytoBandIdeo.as
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cytoBandIdeo.as	Wed May 31 11:35:16 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
diff -r 2677f1899aa8 -r fcc1021bd496 hubArchiveCreator.py
--- a/hubArchiveCreator.py	Tue May 09 15:42:43 2017 -0400
+++ b/hubArchiveCreator.py	Wed May 31 11:35:16 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
@@ -29,6 +30,7 @@
 from TrackHub import TrackHub
 from bigPsl import bigPsl
 from BedBlastAlignments import BedBlastAlignments
+from BigBed import BigBed
 
 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
 
@@ -55,6 +57,9 @@
     # 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')
 
@@ -70,6 +75,9 @@
     # Psl Management
     parser.add_argument('--psl', action='append', help='Psl format')
 
+    # BigBed Management
+    parser.add_argument('--bigbed', action='append', help='BigBed format')
+
     # TODO: Check if the running directory can have issues if we run the tool outside
     parser.add_argument('-d', '--directory',
                         help='Running tool directory, where to find the templates. Default is running directory')
@@ -124,6 +132,7 @@
     # 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
@@ -132,6 +141,7 @@
     array_inputs_psl = args.psl
     array_inputs_bigpsl = args.bigpsl
     array_inputs_bed_blast_alignments = args.bedBlastAlignments
+    array_inputs_bigbed = args.bigbed
 
     outputFile = args.output
 
@@ -152,6 +162,7 @@
     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),
@@ -159,7 +170,8 @@
                         (array_inputs_gtf, Gtf),
                         (array_inputs_psl, Psl),
                         (array_inputs_bigpsl, bigPsl),
-                        (array_inputs_bed_blast_alignments, BedBlastAlignments)]:
+                        (array_inputs_bed_blast_alignments, BedBlastAlignments),
+                        (array_inputs_bigbed, BigBed)]:
         if inputs:
             all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))
 
diff -r 2677f1899aa8 -r fcc1021bd496 hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Tue May 09 15:42:43 2017 -0400
+++ b/hubArchiveCreator.xml	Wed May 31 11:35:16 2017 -0400
@@ -5,8 +5,10 @@
     </description>
 
     <requirements>
-        <requirement type="package" version="1.0">ucsc_tools_340</requirement>
+        <requirement type="package" version="340">ucsc_hac</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="340">ucsc_bigwig</requirement>
+        <requirement type="package" version="340">ucsc_bigbed</requirement>
     </requirements>
 
     <stdio>
@@ -90,6 +92,11 @@
                         #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,
@@ -102,12 +109,12 @@
                     #end if
                     #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
                         --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
-                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,                              
+                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
                                              extra_data_dict)
                     #end if
                     #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
                         --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
-                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,                              
+                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
                                              extra_data_dict)
                     #end if
                 #end if
@@ -121,6 +128,11 @@
                     #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
                                             extra_data_dict)
                 #end if
+                #if $f.formatChoice.format_select == "bigbed"
+                    --bigbed $f.formatChoice.BIGBED
+                    #silent $prepare_json($f.formatChoice.BIGBED, $index_track_final,
+                                            extra_data_dict)
+                #end if
                 #if $f.formatChoice.format_select == "gff3"
                     --gff3 $f.formatChoice.GFF3
                     #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
@@ -180,6 +192,7 @@
                         <option value="bed">BED</option>
                         <option value="psl">PSL</option>
                         <option value="bigwig">BIGWIG</option>
+                        <option value="bigbed">BIGBED</option>
                         <option value="gff3">GFF3</option>
                         <option value="gtf">GTF</option>
                     </param>
@@ -200,11 +213,12 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                    </when>     
+                    </when>
                     <when value="bed">
                         <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>
@@ -219,6 +233,14 @@
                                 />
 
                             </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"
@@ -293,6 +315,22 @@
                             </sanitizer>
                         </param>
                     </when>
+                    <when value="bigbed">
+                        <param
+                                format="bigbed"
+                                name="BIGBED"
+                                type="data"
+                                label="BIGBED File"
+                        />
+                        <param name="longLabel" type="text" size="30" label="Track name" />
+                        <param name="track_color" type="color" label="Track color" value="#000000">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                    <add value="#"/>
+                                </valid>
+                            </sanitizer>
+                        </param>
+                    </when>
                     <when value="gff3">
                         <param
                                 format="gff3"
@@ -474,7 +512,7 @@
                 />
             </output>
         </test>
-        
+
 
         <!-- Test with Psl -->
         <test>
@@ -1029,4 +1067,8 @@
         This Galaxy tool permits to prepare your files to be ready for
         Assembly Hub visualization.
     </help>
+
+    <citations>
+        <citation type="doi">10.7490/f1000research.1112719.1</citation>
+    </citations>
 </tool>
diff -r 2677f1899aa8 -r fcc1021bd496 templates/trackDb/layout.txt
--- a/templates/trackDb/layout.txt	Tue May 09 15:42:43 2017 -0400
+++ b/templates/trackDb/layout.txt	Wed May 31 11:35:16 2017 -0400
@@ -1,14 +1,32 @@
 % for trackDb in trackDbs:
-    ## See this http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
-    track ${trackDb.trackName}
-    longLabel ${trackDb.longLabel}
-    shortLabel ${trackDb.shortLabel}
-    bigDataUrl ${trackDb.trackDataURL}
-    type ${trackDb.trackType}
-    visibility ${trackDb.visibility}
-    thickDrawItem ${trackDb.thickDrawItem}
-    priority ${trackDb.priority}
-    color ${trackDb.track_color}
-    group ${trackDb.group_name.lower().replace(' ', '_')}
+    % if "bigWig" in trackDb.trackType:
+
+track ${trackDb.trackName}
+longLabel ${trackDb.longLabel}
+shortLabel ${trackDb.shortLabel}
+bigDataUrl ${trackDb.trackDataURL}
+visibility ${trackDb.visibility}
+priority ${trackDb.priority}
+color ${trackDb.track_color}
+group ${trackDb.group_name.lower().replace(' ', '_')}
+type ${trackDb.trackType}
+autoScale on
+maxHeightPixels 100:32:8
+windowingFunction mean+whiskers
 
+    % else:
+
+## See this http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
+track ${trackDb.trackName}
+longLabel ${trackDb.longLabel}
+shortLabel ${trackDb.shortLabel}
+bigDataUrl ${trackDb.trackDataURL}
+type ${trackDb.trackType}
+visibility ${trackDb.visibility}
+thickDrawItem ${trackDb.thickDrawItem}
+priority ${trackDb.priority}
+color ${trackDb.track_color}
+group ${trackDb.group_name.lower().replace(' ', '_')}
+
+    % endif
 % endfor
diff -r 2677f1899aa8 -r fcc1021bd496 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 09 15:42:43 2017 -0400
+++ b/tool_dependencies.xml	Wed May 31 11:35:16 2017 -0400
@@ -1,6 +1,5 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <!-- UCSC Tools in  -->
     <!-- Useful for HAC are:
         - twoBitInfo
         - sort
@@ -16,23 +15,15 @@
     <package name="samtools" version="1.2">
         <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    
-    <package name="ucsc_tools_340" version="1.0">
-        <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>                       
-                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                    </action>    
-                </actions>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions_group>
-         </install>
-         <readme>The well known UCSC tools from Jim Kent.</readme>
+    <package name="ucsc_hac" version="340">
+        <repository changeset_revision="a819439b6d76" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ucsc_bigbed" version="340">
+        <repository changeset_revision="b23d341df89d" name="package_ucsc_bigbed_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    
+
+    <package name="ucsc_bigwig" version="340">      
+        <repository changeset_revision="b1fb46f92da0" name="package_ucsc_bigwig_340" owner="yating-l" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
 </tool_dependency>
diff -r 2677f1899aa8 -r fcc1021bd496 util/subtools.py
--- a/util/subtools.py	Tue May 09 15:42:43 2017 -0400
+++ b/util/subtools.py	Wed May 31 11:35:16 2017 -0400
@@ -250,6 +250,8 @@
 # See the "track" Common settings at:
 #https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments
 def fixName(filename):
+    if filename == 'cytoBandIdeo':
+        return filename
     valid_chars = "_%s%s" % (string.ascii_letters, string.digits)
     sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename])
     sanitize_name = "gonramp_" + sanitize_name