From 80d30e42257a5c3c1847117df088d1f40c13d843 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 30 Mar 2011 14:31:22 -0700 Subject: [PATCH] Update single vs paired guessing code Add in new guesses for Georgi files to view names --- extra/ucsc_encode_submission/ucsc_gather.py | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py index 90b4b35..38d8dee 100755 --- 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 = [ + # 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), @@ -751,8 +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 -- 2.30.2