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Fast(er) SAM set_meta that follows a 12-field predefined format.

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Dannon Baker
2010-12-01 09:30:48 -05:00
parent 1190341469
commit 7cd396bd65
1 changed files with 13 additions and 0 deletions
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lib/galaxy/datatypes/tabular.py
+13
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@@ -356,6 +356,19 @@ class Sam( Tabular ):
pass
return False
def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = 5, **kwd ):
if dataset.has_data():
dataset_fh = open( dataset.file_name )
comment_lines = 0
for i, l in enumerate(dataset_fh):
if l.startswith('@'):
comment_lines += 1
dataset_fh.close()
dataset.metadata.data_lines = i + 1 - comment_lines
dataset.metadata.comment_lines = comment_lines
dataset.metadata.columns = 12
dataset.metadata.column_types = ['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']
class Pileup( Tabular ):
"""Tab delimited data in pileup (6- or 10-column) format"""
file_ext = "pileup"