Update single vs paired guessing code

[htsworkflow.git] / extra / ucsc_encode_submission / ucsc_gather.py

diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py
index 7650a9468e96df9486ec98e3e0721d90a46ff3de..38d8deefc7a8a1b2dc07b3f445534d24fc4fef0d 100755 (executable)
--- a/extra/ucsc_encode_submission/ucsc_gather.py
+++ b/extra/ucsc_encode_submission/ucsc_gather.py
@@ -37,10 +37,7 @@ def main(cmdline=None):
     else:
         logging.basicConfig(level = logging.WARNING )        
     
-    apidata = {'apiid': opts.apiid, 'apikey': opts.apikey }
-
-    if opts.host is None or opts.apiid is None or opts.apikey is None:
-        parser.error("Please specify host url, apiid, apikey")
+    apidata = api.make_auth_from_opts(opts, parser)
 
     if opts.makeddf and opts.daf is None:
         parser.error("Please specify your daf when making ddf files")
@@ -73,22 +70,6 @@ def main(cmdline=None):
 
 
 def make_parser():
-    # Load defaults from the config files
-    config = SafeConfigParser()
-    config.read([os.path.expanduser('~/.htsworkflow.ini'), '/etc/htsworkflow.ini'])
-    
-    sequence_archive = None
-    apiid = None
-    apikey = None
-    apihost = None
-    SECTION = 'sequence_archive'
-    if config.has_section(SECTION):
-        sequence_archive = config.get(SECTION, 'sequence_archive',sequence_archive)
-        sequence_archive = os.path.expanduser(sequence_archive)
-        apiid = config.get(SECTION, 'apiid', apiid)
-        apikey = config.get(SECTION, 'apikey', apikey)
-        apihost = config.get(SECTION, 'host', apihost)
-
     parser = OptionParser()
 
     # commands
@@ -108,20 +89,14 @@ def make_parser():
     parser.add_option('--force', default=False, action="store_true",
                       help="Force regenerating fastqs")
 
-    # configuration options
-    parser.add_option('--apiid', default=apiid, help="Specify API ID")
-    parser.add_option('--apikey', default=apikey, help="Specify API KEY")
-    parser.add_option('--host',  default=apihost,
-                      help="specify HTSWorkflow host",)
-    parser.add_option('--sequence', default=sequence_archive,
-                      help="sequence repository")
-
     # debugging
     parser.add_option('--verbose', default=False, action="store_true",
                       help='verbose logging')
     parser.add_option('--debug', default=False, action="store_true",
                       help='debug logging')
 
+    api.add_auth_options(parser)
+    
     return parser
 
 
@@ -650,6 +625,18 @@ class NameToViewMap(object):
         ma = 'TH1014'
 
         self.patterns = [
+            # for 2011 Feb 18 elements submission
+            ('final_Cufflinks_genes_*gtf',       'GeneDeNovo'),
+            ('final_Cufflinks_transcripts_*gtf', 'TranscriptDeNovo'),
+            ('final_exonFPKM-Cufflinks-0.9.3-GENCODE-v3c-*.gtf',       
+             'ExonsGencV3c'),
+            ('final_GENCODE-v3-Cufflinks-0.9.3.genes-*gtf',          
+             'GeneGencV3c'),
+            ('final_GENCODE-v3-Cufflinks-0.9.3.transcripts-*gtf',    
+             'TranscriptGencV3c'),
+            ('final_TSS-Cufflinks-0.9.3-GENCODE-v3c-*.gtf', 'TSS'),
+            ('final_junctions-*.bed6+3',                    'Junctions'),
+            
             ('*.bai',                   None),
             ('*.splices.bam',           'Splices'),
             ('*.bam',                   self._guess_bam_view),
@@ -663,9 +650,19 @@ class NameToViewMap(object):
             ('*.condor',                None),
             ('*.daf',                   None),
             ('*.ddf',                   None),
+
+            ('*ufflinks?0.9.3.genes.gtf',       'GeneDeNovo'),
+            ('*ufflinks?0.9.3.transcripts.gtf', 'TranscriptDeNovo'),
+            ('*GENCODE-v3c.exonFPKM.gtf',        'ExonsGencV3c'),
+            ('*GENCODE-v3c.genes.gtf',           'GeneGencV3c'),
+            ('*GENCODE-v3c.transcripts.gtf',     'TranscriptGencV3c'),
+            ('*GENCODE-v3c.TSS.gtf',             'TSS'),
+            ('*.junctions.bed6+3',                'Junctions'),
+            
             ('*.?ufflinks-0.9.0?genes.expr',       'GeneDeNovo'),
             ('*.?ufflinks-0.9.0?transcripts.expr', 'TranscriptDeNovo'),
             ('*.?ufflinks-0.9.0?transcripts.gtf',  'GeneModel'),
+
             ('*.GENCODE-v3c?genes.expr',       'GeneGCV3c'),
             ('*.GENCODE-v3c?transcript*.expr', 'TranscriptGCV3c'),
             ('*.GENCODE-v3c?transcript*.gtf',  'TranscriptGencV3c'),
@@ -686,6 +683,7 @@ class NameToViewMap(object):
             ('*.srf',                   None),
             ('*.wig',                   None),
             ('*.zip',                   None),
+            ('transfer_log',            None),
             ]
 
         self.views = {
@@ -701,6 +699,9 @@ class NameToViewMap(object):
             "GeneModel": {"MapAlgorithm": ma},
             "GeneDeNovo": {"MapAlgorithm": ma},
             "TranscriptDeNovo": {"MapAlgorithm": ma},
+            "ExonsGencV3c": {"MapAlgorithm": ma},
+            "GeneGencV3c": {"MapAlgorithm": ma},
+            "TSS": {"MapAlgorithm": ma},
             "GeneGCV3c": {"MapAlgorithm": ma},
             "TranscriptGCV3c": {"MapAlgorithm": ma},
             "TranscriptGencV3c": {"MapAlgorithm": ma},
@@ -762,8 +763,14 @@ class NameToViewMap(object):
 
     def _is_paired(self, lib_id, lib_info):
         """Determine if a library is paired end"""
+        # TODO: encode this information in the library type page.
+        single = (1,3,6)
         if len(lib_info["lane_set"]) == 0:
-            return False
+            # we haven't sequenced anything so guess based on library type
+            if lib_info['library_type_id'] in single:
+                return False
+            else:
+                return True
 
         if not self.lib_paired.has_key(lib_id):
             is_paired = 0