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Update single vs paired guessing code
author
Diane Trout
<diane@caltech.edu>
Wed, 30 Mar 2011 21:31:22 +0000
(14:31 -0700)
committer
Diane Trout
<diane@caltech.edu>
Wed, 30 Mar 2011 21:31:22 +0000
(14:31 -0700)
Add in new guesses for Georgi files to view names
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 90b4b3568b360ab120ad74c02c210cd5cbba822b..38d8deefc7a8a1b2dc07b3f445534d24fc4fef0d 100755
(executable)
--- a/
extra/ucsc_encode_submission/ucsc_gather.py
+++ b/
extra/ucsc_encode_submission/ucsc_gather.py
@@
-625,6
+625,18
@@
class NameToViewMap(object):
ma = 'TH1014'
self.patterns = [
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),
('*.bai', None),
('*.splices.bam', 'Splices'),
('*.bam', self._guess_bam_view),
@@
-751,8
+763,14
@@
class NameToViewMap(object):
def _is_paired(self, lib_id, lib_info):
"""Determine if a library is paired end"""
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:
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
if not self.lib_paired.has_key(lib_id):
is_paired = 0