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Add in patterns for Encode Elements submission
author
Diane Trout
<diane@caltech.edu>
Wed, 16 Feb 2011 19:06:34 +0000
(11:06 -0800)
committer
Diane Trout
<diane@caltech.edu>
Wed, 16 Feb 2011 23:15:20 +0000
(15:15 -0800)
extra/ucsc_encode_submission/ucsc_gather.py
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diff --git
a/extra/ucsc_encode_submission/ucsc_gather.py
b/extra/ucsc_encode_submission/ucsc_gather.py
index 7650a9468e96df9486ec98e3e0721d90a46ff3de..07bea2c495b9d2d02309ec270cc7a9f1b0f3c1f0 100755
(executable)
--- a/
extra/ucsc_encode_submission/ucsc_gather.py
+++ b/
extra/ucsc_encode_submission/ucsc_gather.py
@@
-663,9
+663,19
@@
class NameToViewMap(object):
('*.condor', None),
('*.daf', None),
('*.ddf', None),
('*.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'),
('*.?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'),
('*.GENCODE-v3c?genes.expr', 'GeneGCV3c'),
('*.GENCODE-v3c?transcript*.expr', 'TranscriptGCV3c'),
('*.GENCODE-v3c?transcript*.gtf', 'TranscriptGencV3c'),
@@
-686,6
+696,7
@@
class NameToViewMap(object):
('*.srf', None),
('*.wig', None),
('*.zip', None),
('*.srf', None),
('*.wig', None),
('*.zip', None),
+ ('transfer_log', None),
]
self.views = {
]
self.views = {
@@
-701,6
+712,9
@@
class NameToViewMap(object):
"GeneModel": {"MapAlgorithm": ma},
"GeneDeNovo": {"MapAlgorithm": ma},
"TranscriptDeNovo": {"MapAlgorithm": ma},
"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},
"GeneGCV3c": {"MapAlgorithm": ma},
"TranscriptGCV3c": {"MapAlgorithm": ma},
"TranscriptGencV3c": {"MapAlgorithm": ma},