Georgi used slightly different extensions for the second batch

of data

diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py
index 7480231da794f01b8813bca93d13f6ddd15c9a94..3830dbef7d49b0f78d820662c0e1aaadf01335ee 100755 (executable)
--- a/extra/ucsc_encode_submission/ucsc_gather.py
+++ b/extra/ucsc_encode_submission/ucsc_gather.py
@@ -257,10 +257,13 @@ def make_submission_ini(host, apidata, library_result_map, paired=True):
      '.condor':                {'view': None},
      '.daf':                   {'view': None},
      '.ddf':                   {'view': None},
+     'denovo.genes.expr':       {'view': 'GeneDeNovo', 'MapAlgorithm': ma},
+     'denovo.transcripts.expr': {'view': 'TranscriptDeNovo', 'MapAlgorithm': ma},
      'novel.genes.expr':       {'view': 'GeneDeNovo', 'MapAlgorithm': ma},
      'novel.transcripts.expr': {'view': 'TranscriptDeNovo', 'MapAlgorithm': ma},
      '.genes.expr':            {'view': 'GeneFPKM', 'MapAlgorithm': ma},
      '.transcripts.expr':      {'view': 'TranscriptFPKM', 'MapAlgorithm': ma},
+     '.transcript.expr':       {'view': 'TranscriptFPKM', 'MapAlgorithm': ma},
      '.fastq':                 {'view': 'Fastq', 'MapAlgorithm': 'NA' },
      '_r1.fastq':              {'view': 'FastqRd1', 'MapAlgorithm': 'NA'},
      '_r2.fastq':              {'view': 'FastqRd2', 'MapAlgorithm': 'NA'},