Binary file Bam.pyc has changed

--- a/Bed.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/Bed.py	Thu Aug 11 19:02:29 2016 -0400
@@ -33,7 +33,9 @@
 
         myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
         with open(myBigBedFilePath, 'w') as self.bigBedFile:
-            subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name)
+            subtools.bedToBigBed(self.sortedBedFile.name,
+                                 self.chromSizesFile.name,
+                                 self.bigBedFile.name)
 
         # Create the Track Object
         self.createTrack(file_path=trackName,

Binary file Bed.pyc has changed

--- a/BedSimpleRepeats.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/BedSimpleRepeats.py	Thu Aug 11 19:02:29 2016 -0400
@@ -27,10 +27,14 @@
         # TODO: Change the name of the bb, to tool + genome + .bb
         trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
         myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
-        auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as'))
+
+        auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as')
+
         with open(myBigBedFilePath, 'w') as bigBedFile:
-            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name,
-                                 typeOption='-type=bed4+12',
+            subtools.bedToBigBed(sortedBedFile.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 typeOption='bed4+12',
                                  autoSql=auto_sql_option)
 
         # Create the Track Object

Binary file BedSimpleRepeats.pyc has changed

--- a/BigWig.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/BigWig.py	Thu Aug 11 19:02:29 2016 -0400
@@ -29,7 +29,8 @@
         # Create the Track Object
         self.createTrack(file_path=trackName,
                          track_name=trackName,
-                         long_label=self.name_bigwig, track_type='bigWig', visibility='full',
+                         long_label=self.name_bigwig,
+                         track_type='bigWig', visibility='full',
                          priority=self.priority,
                          track_file=myBigWigFilePath)
 

Binary file BigWig.pyc has changed

--- a/Datatype.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/Datatype.py	Thu Aug 11 19:02:29 2016 -0400
@@ -40,8 +40,6 @@
         if Datatype.tool_directory is None:
             raise TypeError(not_init_message.format('tool directory'))
 
-
-
     @staticmethod
     def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
                  extra_files_path, tool_directory, specie_folder, tracks_folder):

Binary file Datatype.pyc has changed

--- a/Gff3.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/Gff3.py	Thu Aug 11 19:02:29 2016 -0400
@@ -21,53 +21,42 @@
         self.priority = data_gff3["order_index"]
 
         # TODO: See if we need these temporary files as part of the generated files
-        genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
-        unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
-        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
-
-        # TODO: Refactor into another Class to manage the twoBitInfo and ChromSizes (same process as in Gtf.py)
+        unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
+        unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
+        sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
 
         # gff3ToGenePred processing
-        subtools.gff3ToGenePred(self.input_Gff3_false_path, genePredFile.name)
+        subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name)
 
-        # TODO: From there, refactor because common use with Gtf.py
-        # genePredToBed processing
-        subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)
+        # genePredToBigGenePred
+        subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name)
 
         # Sort processing
-        subtools.sort(unsortedBedFile.name, sortedBedFile.name)
+        subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name)
 
         # TODO: Check if no errors
 
         # bedToBigBed processing
-        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
         trackName = "".join( (self.name_gff3, ".bb" ) )
+
+        auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
+
         myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
         with open(myBigBedFilePath, 'w') as bigBedFile:
-            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
+            subtools.bedToBigBed(sorted_biGenePred_file.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 autoSql=auto_sql_option,
+                                 typeOption='bed12+8',
+                                 tab=True)
 
         # Create the Track Object
         self.createTrack(file_path=trackName,
                          track_name=trackName,
-                         long_label=self.name_gff3, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
+                         long_label=self.name_gff3,
+                         track_type='bigGenePred', visibility='dense',
+                         priority=self.priority,
                          track_file=myBigBedFilePath)
 
-        # dataURL = "tracks/%s" % trackName
-        #
-        # trackDb = TrackDb(
-        #     trackName=trackName,
-        #     longLabel=self.name_gff3,
-        #     shortLabel=self.getShortName( self.name_gff3 ),
-        #     trackDataURL=dataURL,
-        #     trackType='bigBed 12 +',
-        #     visibility='dense',
-        #     priority=self.priority,
-        # )
-        #
-        # self.track = Track(
-        #     trackFile=myBigBedFilePath,
-        #     trackDb=trackDb,
-        # )
-
         print("- Gff3 %s created" % self.name_gff3)
-        #print("- %s created in %s" % (trackName, myBigBedFilePath))

Binary file Gff3.pyc has changed

--- a/Gtf.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/Gtf.py	Thu Aug 11 19:02:29 2016 -0400
@@ -25,47 +25,40 @@
 
         # TODO: See if we need these temporary files as part of the generated files
         genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
-        unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
-        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
+        unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
+        sorted_bigGenePred_file = tempfile.NamedTemporaryFile(suffix=".sortedBed.bigGenePred")
 
         # GtfToGenePred
         subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)
 
         # TODO: From there, refactor because common use with Gff3.py
-        #  genePredToBed processing
-        subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)
+        # genePredToBigGenePred processing
+        subtools.genePredToBigGenePred(genePredFile.name, unsorted_bigGenePred_file.name)
 
         # Sort processing
-        subtools.sort(unsortedBedFile.name, sortedBedFile.name)
+        subtools.sort(unsorted_bigGenePred_file.name, sorted_bigGenePred_file.name)
 
         # bedToBigBed processing
-        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
         trackName = "".join( ( self.name_gtf, ".bb") )
+
+        auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
+
         myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
         with open(myBigBedFilePath, 'w') as bigBedFile:
-            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
+            subtools.bedToBigBed(sorted_bigGenePred_file.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 autoSql=auto_sql_option,
+                                 typeOption='bed12+8',
+                                 tab=True)
+
 
         # Create the Track Object
         self.createTrack(file_path=trackName,
                          track_name=trackName,
-                         long_label=self.name_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
+                         long_label=self.name_gtf, track_type='bigGenePred',
+                         visibility='dense', priority=self.priority,
                          track_file=myBigBedFilePath)
-        #
-        # dataURL = "tracks/%s" % trackName
-        #
-        # trackDb = TrackDb(
-        #     trackName=trackName,
-        #     longLabel=self.name_gtf,
-        #     shortLabel=self.getShortName( self.name_gtf ),
-        #     trackDataURL=dataURL,
-        #     trackType='bigBed 12 +',
-        #     visibility='dense',
-        #     priority=self.priority,
-        # )
-        # self.track = Track(
-        #     trackFile=myBigBedFilePath,
-        #     trackDb=trackDb,
-        # )
 
         print("- Gtf %s created" % self.name_gtf)
-        #print("- %s created in %s" % (trackName, myBigBedFilePath))

Binary file Gtf.pyc has changed

Binary file TrackDb.pyc has changed

Binary file TrackHub.pyc has changed

--- a/__init__.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/__init__.py	Thu Aug 11 19:02:29 2016 -0400
@@ -0,0 +1,19 @@
+# Set default logging handler to avoid "No handler found" warnings.
+import logging
+import sys
+
+try:  # Python 2.7+
+    from logging import NullHandler
+except ImportError:
+    class NullHandler(logging.Handler):
+        def emit(self, record):
+            pass
+
+logging.getLogger(__name__).addHandler(NullHandler())
+
+log_stdout = None
+log_stderr = None
+
+
+# TODO: Handle the Exception by dispatching the error depending on the (debug) mode
+#class Exception(Exception):
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigGenePred.as	Thu Aug 11 19:02:29 2016 -0400
@@ -0,0 +1,25 @@
+table bigGenePred
+"bigGenePred gene models"
+   (
+   string chrom;       "Reference sequence chromosome or scaffold"
+   uint   chromStart;  "Start position in chromosome"
+   uint   chromEnd;    "End position in chromosome"
+   string name;        "Name or ID of item, ideally both human readable and unique"
+   uint score;         "Score (0-1000)"
+   char[1] strand;     "+ or - for strand"
+   uint thickStart;    "Start of where display should be thick (start codon)"
+   uint thickEnd;      "End of where display should be thick (stop codon)"
+   uint reserved;       "RGB value (use R,G,B string in input file)"
+   int blockCount;     "Number of blocks"
+   int[blockCount] blockSizes; "Comma separated list of block sizes"
+   int[blockCount] chromStarts; "Start positions relative to chromStart"
+   string name2;       "Alternative/human readable name"
+   string cdsStartStat; "Status of CDS start annotation (none, unknown, incomplete, or complete)"
+   string cdsEndStat;   "Status of CDS end annotation (none, unknown, incomplete, or complete)"
+   int[blockCount] exonFrames; "Exon frame {0,1,2}, or -1 if no frame for exon"
+   string type;        "Transcript type"
+   string geneName;    "Primary identifier for gene"
+   string geneName2;   "Alternative/human readable gene name"
+   string geneType;    "Gene type"
+   )
+

--- a/hubArchiveCreator.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/hubArchiveCreator.py	Thu Aug 11 19:02:29 2016 -0400
@@ -11,6 +11,8 @@
 import argparse
 import collections
 import json
+import logging
+import os
 import sys
 
 # Internal dependencies
@@ -19,11 +21,11 @@
 from Bed import Bed
 from BigWig import BigWig
 from util.Fasta import Fasta
+from util.Filters import TraceBackFormatter
 from Gff3 import Gff3
 from Gtf import Gtf
 from TrackHub import TrackHub
 
-
 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
 
 
@@ -67,7 +69,9 @@
 
     parser.add_argument('--genome_name', help='UCSC Genome Browser assembly ID')
 
-    ucsc_tools_path = ''
+    parser.add_argument('--debug_mode', action='store_true', help='Allow more details about the errors')
+
+    # Begin init variables
 
     toolDirectory = '.'
     extra_files_path = '.'
@@ -75,6 +79,16 @@
     # Get the args passed in parameter
     args = parser.parse_args()
 
+    extra_files_path = args.extra_files_path
+    toolDirectory = args.directory
+
+    #### Logging management ####
+    # If we are in Debug mode, also print in stdout the debug dump
+
+    configure_logger(extra_files_path=extra_files_path, debug=args.debug_mode)
+
+    #### END Logging management ####
+
     array_inputs_reference_genome = json.loads(args.fasta)
 
     # TODO: Replace these with the object Fasta
@@ -100,7 +114,6 @@
     array_inputs_bigwig = args.bigwig
 
     outputFile = args.output
-    json_inputs_data = args.data_json
 
     json_inputs_data = args.data_json
 
@@ -108,10 +121,6 @@
     # We remove the spaces in ["name"] of inputs_data
     sanitize_name_inputs(inputs_data)
 
-    if args.directory:
-        toolDirectory = args.directory
-    if args.extra_files_path:
-        extra_files_path = args.extra_files_path
 
     # TODO: Check here all the binaries / tools we need. Exception if missing
 
@@ -141,9 +150,7 @@
     # We terminate le process and so create a HTML file summarizing all the files
     trackHub.terminate()
 
-    print "\t"
-    print "--------------"
-    print "Well done guys! Your data are ready to be displayed in UCSC Track Hub."
+    logging.debug('#### End of HubArchiveCreator Debug Mode: Bye! ####')
 
     sys.exit(0)
 
@@ -184,5 +191,87 @@
                 datatype_dictionary.update({data_value["order_index"]: extensionObject})
     return datatype_dictionary
 
+def configure_logger(extra_files_path=None, debug=False):
+    if not extra_files_path:
+        raise Exception("Extra files path is not set. Stopping the application")
+
+
+    # All case log: log everything in a .log file
+    logger_file_name = ''.join([__name__, '.log'])
+    logging_file_path = os.path.join(extra_files_path, logger_file_name)
+
+    logging.basicConfig(filename=logging_file_path, level=logging.DEBUG)
+
+    log_stdout = logging.StreamHandler(sys.stdout)
+    if not debug:
+        configure_logger_user(log_stdout)
+    else:
+        configure_logger_dev(log_stdout)
+
+    # stderr configuration
+    configure_logger_stderr()
+
+    logging.debug('#### Welcome in HubArchiveCreator Debug Mode ####\n')
+
+def configure_logger_user(log_stdout=None):
+    """
+    User Logger is defined as following:
+        - User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback
+            in STDOUT
+        - Still access to full, brute and traceback for errors
+            in STDERR
+        - And further access to debug if needed
+            in .log
+    :return:
+    """
+    if not log_stdout:
+        raise Exception("No log_stdout given. Stopping the application")
+
+    # stdout for INFO / WARN / ERROR / CRITICAL
+    log_stdout.setLevel(logging.INFO)
+
+    formatter = TraceBackFormatter('%(message)s')
+
+    log_stdout.setFormatter(formatter)
+
+    logging.getLogger().addHandler(log_stdout)
+
+def configure_logger_dev(log_stdout=None):
+    """
+    Dev Logger is defined as following:
+        - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout
+        - Still access to full, brute and traceback in stderr for errors
+        - And further access to debug if needed
+    :return:
+    """
+    if not log_stdout:
+        raise Exception("No log_stdout given. Stopping the application")
+    log_format = '%(message)s'
+
+    # stdout and stderr and both identical for INFO / WARN / ERROR / CRITICAL
+    log_stdout.setLevel(logging.DEBUG)
+
+    formatter = logging.Formatter(log_format)
+
+    log_stdout.setFormatter(formatter)
+
+    logging.getLogger().addHandler(log_stdout)
+
+def configure_logger_stderr():
+    """
+    Configure what should be logged in stderr
+    :return:
+    """
+    log_error = logging.StreamHandler(sys.stderr)
+    log_error.setLevel(logging.ERROR)
+    log_error_format = '%(message)s'
+
+    formatter_error = logging.Formatter(log_error_format)
+
+    log_error.setFormatter(formatter_error)
+
+    logging.getLogger().addHandler(log_error)
+
 if __name__ == "__main__":
+    logging.getLogger(__name__)
     main(sys.argv)

--- a/hubArchiveCreator.xml	Wed Jul 27 10:43:58 2016 -0400
+++ b/hubArchiveCreator.xml	Thu Aug 11 19:02:29 2016 -0400
@@ -14,6 +14,7 @@
         <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
         <requirement type="package" version="332">ucsc-fatotwobit</requirement>
         <requirement type="package" version="324">ucsc-genepredtobed</requirement>
+        <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
         <requirement type="package" version="324">ucsc-gff3togenepred</requirement>
         <requirement type="package" version="324">ucsc-gtftogenepred</requirement>
         <requirement type="package" version="324">ucsc-twobitinfo</requirement>
@@ -99,7 +100,13 @@
         ## Retrieve the user email
         --user_email $__user_email__
 
-        -d $__tool_directory__ -e $output.files_path -o $output;
+        -d $__tool_directory__
+
+        -e $output.files_path
+
+        $advanced_options.debug_mode
+
+        -o $output;
     ]]></command>
 
     <inputs>
@@ -184,7 +191,28 @@
                 </when>
             </conditional>
         </repeat>
-    </inputs>
+        <conditional name="advanced_options">
+            <param name="advanced_options_selector" type="select" label="Advanced options">
+                <option value="off" selected="true">Hide advanced options</option>
+                <option value="on">Display advanced options</option>
+            </param>
+            <!-- TODO: Avoid redundancy here -->
+            <when value="on">
+                <param name="debug_mode" type="boolean"
+                       label="Activate debug mode" checked="false"
+                       truevalue="--debug_mode" falsevalue="">
+                    <help>
+                        Use this option if you are a G-OnRamp developer
+                    </help>
+                </param>
+            </when>
+            <when value="off">
+                <param name="debug_mode" type="hidden"
+                       value="">
+                </param>
+            </when>
+    </conditional>
+</inputs>
 
     <outputs>
         <data format="trackhub" name="output"/>

--- a/todo.md	Wed Jul 27 10:43:58 2016 -0400
+++ b/todo.md	Thu Aug 11 19:02:29 2016 -0400
@@ -1,10 +1,44 @@
+### 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*
 
 ### TO COMPLETE
 
- 
+
 - [ ] 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:

Binary file util/Fasta.pyc has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/Filters.py	Thu Aug 11 19:02:29 2016 -0400
@@ -0,0 +1,9 @@
+import logging
+
+class TraceBackFormatter(logging.Formatter):
+    def format(self, record):
+        # If the log has some Exception text, we don't display them
+        s = super(TraceBackFormatter, self).format(record)
+        if record.exc_text or record.exc_info:
+            s = record.message
+        return s

Binary file util/Filters.pyc has changed

--- a/util/subtools.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/util/subtools.py	Thu Aug 11 19:02:29 2016 -0400
@@ -6,9 +6,21 @@
 in HubArchiveCreator
 """
 
+import logging
 import os
 import subprocess
+import sys
 
+class PopenError(Exception):
+    def __init__(self, cmd, error, return_code):
+        self.cmd = cmd
+        self.error = error
+        self.return_code = return_code
+
+    def __str__(self):
+        message = "The subprocess {0} has returned the error: {1}.".format(self.cmd, self.return_code)
+        message = ','.join((message, "Its error message is: {0}".format(self.error)))
+        return repr(message)
 
 def _handleExceptionAndCheckCall(array_call, **kwargs):
     """
@@ -20,10 +32,47 @@
     stdout = kwargs.get('stdout')
     stderr = kwargs.get('stderr')
     shell = kwargs.get('shell')
+
+    cmd = array_call[0]
+
+    output = None
+    error = None
+
+    # TODO: Check the value of array_call and <=[0]
+    logging.debug("Calling {0}:".format(cmd))
+
+    logging.debug("---------")
+
+    # TODO: Use universal_newlines option from Popen?
     try:
-        p = subprocess.check_call(array_call, stdin=stdin, stdout=stdout, stderr=stderr, shell=shell)
-    except subprocess.CalledProcessError:
-        raise
+        p = subprocess.Popen(array_call, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=shell)
+        output, error = p.communicate()
+
+        logging.debug("\t{0}".format(output))
+        # If we detect an error from the subprocess, then we raise an exception
+        # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
+        # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
+        if p.returncode:
+            raise PopenError(cmd, error, p.returncode)
+
+    except OSError as e:
+        message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)
+        if e.filename:
+            message = '\n'.join((message, ", against this file: {0}".format(e.filename)))
+        logging.error(message)
+        sys.exit(-1)
+    except PopenError as p:
+        message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)
+        message = '\n'.join((message, "Its error message is: {0}".format(p.error)))
+
+        logging.exception(message)
+
+        sys.exit(p.return_code)
+    except Exception as e:
+        message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)
+        logging.exception(message)
+
+        sys.exit(-1)
     return p
 
 
@@ -76,6 +125,18 @@
     p = _handleExceptionAndCheckCall(array_call)
     return p
 
+def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
+    """
+    Call genePredToBigGenePred and write the result into unsorted_bigGenePred_file_name
+    :param gene_pred_file_name:
+    :param unsorted_bigGenePred_file_name:
+    :return:
+    """
+    array_call = ['genePredToBigGenePred',
+                  gene_pred_file_name,
+                  unsorted_bigGenePred_file_name]
+    p = _handleExceptionAndCheckCall(array_call)
+    return p
 
 def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
     """
@@ -113,7 +174,8 @@
     return p
 
 
-def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name, typeOption=None, autoSql=None):
+def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name,
+                typeOption=None, autoSql=None, tab=False):
     """
     Call bedToBigBed on sorted_bed_file_name, using chrom_sizes_file_name and write the result into big_bed_file_name
     :param sorted_bed_file_name:
@@ -121,11 +183,25 @@
     :param big_bed_file_name:
     :return:
     """
+
+    # TODO: Move this into the _handleExceptionAndCheckCall function
+    # Parse the array
+    logging.debug("sorted_bed_file_name: {0}".format(sorted_bed_file_name))
+    logging.debug("chrom_sizes_file_name: {0}".format(chrom_sizes_file_name))
+    logging.debug("big_bed_file_name: {0}".format(big_bed_file_name))
+    logging.debug("typeOption: {0}".format(typeOption))
+    logging.debug("autoSql: {0}".format(autoSql))
+    logging.debug("tab option: {0}".format(tab))
+
     array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
     if typeOption:
+        typeOption = ''.join(['-type=', typeOption])
         array_call.append(typeOption)
     if autoSql:
+        autoSql = ''.join(['-as=', autoSql])
         array_call.append(autoSql)
+    if tab:
+        array_call.append('-tab')
 
     p = _handleExceptionAndCheckCall(array_call)
     return p

Binary file util/subtools.pyc has changed