From: Diane Trout <diane@caltech.edu>
Date: Fri, 21 Jan 2011 23:23:29 +0000 (-0800)
Subject: Update view names as per Cricket for the Jan 21st encode submission.
X-Git-Tag: 0.5.1~13^2
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=16ceaf7610ab7879e43fd44b926dba6f3590f549

Update view names as per Cricket for the Jan 21st encode submission.
Also we're avoiding submitting the GENCODE v4 models for this
submission so I commented them out
---

diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py
index 4cea711..dc5fe18 100755
--- a/extra/ucsc_encode_submission/ucsc_gather.py
+++ b/extra/ucsc_encode_submission/ucsc_gather.py
@@ -628,6 +628,7 @@ class NameToViewMap(object):
             ('*.bam',                   self._guess_bam_view),
             ('junctions.bed',           'Junctions'),
             ('*.jnct',                  'Junctions'),
+            ('*.unique.bigwig',         None),
             ('*.plus.bigwig',           'PlusSignal'),
             ('*.minus.bigwig',          'MinusSignal'),
             ('*.bigwig',                'Signal'),
@@ -638,11 +639,12 @@ class NameToViewMap(object):
             ('*.?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',       'GeneGencV3c'),
-            ('*.GENCODE-v3c?transcripts.expr', 'TranscriptGencV3c'),
-            ('*.GENCODE-v4?genes.expr',       'GeneGencV4'),
-            ('*.GENCODE-v4?transcripts.expr', 'TranscriptGencV4'),
-            ('*.GENCODE-v4?transcript.expr', 'TranscriptGencV4'),
+            ('*.GENCODE-v3c?genes.expr',       'GeneGCV3c'),
+            ('*.GENCODE-v3c?transcript*.expr', 'TranscriptGCV3c'),
+            ('*.GENCODE-v3c?transcript*.gtf',  'TranscriptGencV3c'),
+            ('*.GENCODE-v4?genes.expr',        None), #'GeneGCV4'),
+            ('*.GENCODE-v4?transcript*.expr',  None), #'TranscriptGCV4'),
+            ('*.GENCODE-v4?transcript*.gtf',   None), #'TranscriptGencV4'),
             ('*_1.75mers.fastq',              'FastqRd1'),
             ('*_2.75mers.fastq',              'FastqRd2'),
             ('*_r1.fastq',              'FastqRd1'),
@@ -671,14 +673,14 @@ class NameToViewMap(object):
             "GeneModel": {"MapAlgorithm": ma},
             "GeneDeNovo": {"MapAlgorithm": ma},
             "TranscriptDeNovo": {"MapAlgorithm": ma},
-            "GeneGencV3c": {"MapAlgorithm": ma},
+            "GeneGCV3c": {"MapAlgorithm": ma},
+            "TranscriptGCV3c": {"MapAlgorithm": ma},
             "TranscriptGencV3c": {"MapAlgorithm": ma},
-            "GeneGencV4": {"MapAlgorithm": ma},
-            "TranscriptGencV4": {"MapAlgorithm": ma},
+            "GeneGCV4": {"MapAlgorithm": ma},
+            "TranscriptGCV4": {"MapAlgorithm": ma},
             "FastqRd1": {"MapAlgorithm": "NA", "type": "fastq"},
             "FastqRd2": {"MapAlgorithm": "NA", "type": "fastq"},
             "Fastq": {"MapAlgorithm": "NA", "type": "fastq" },
-            "GeneModel": {"MapAlgorithm": ma},
             "InsLength": {"MapAlgorithm": ma},
             }
         # view name is one of the attributes