opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Fix bed.set_meta() to do what it claims it does.

Browse Source 
Other issues with previously existing method:
it only calls tabular.set_meta() if it is a valid bed file
sets dataset.metadata.is_strandCol = "false" , which is not an actual metadata value.
etc
This commit is contained in:
Daniel Blankenberg
2007-10-17 17:40:54 +00:00
parent 74a9f2ecbf
commit fc8a23fa74
1 changed files with 14 additions and 26 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/datatypes/interval.py
+14 -26
View File
@@ -235,33 +235,21 @@ class Bed( Interval ):
files that do not contain a strand column. This will result in changing
the format of the file from BED to Interval.
"""
valid_bed_data = False
i = 0
#initialize tablular metadata
Tabular.set_meta( self, dataset, 0 )
#Use initialized tabular metadata to determine if file fits BED format
bed_col_types = [["str","int"], ["int"], ["int"], ["str"], ["int"], ["str"], ["int"], ["int"], ["int"], ["int"], ["list"], ["list"]]
if dataset.metadata.columns >= 6:
dataset.metadata.strandCol = 6
if dataset.has_data():
for i, line in enumerate( file(dataset.file_name) ):
line = line.rstrip('\r\n')
if line and not line.startswith('#') and len(line) > 0:
elems = line.split('\t')
if len(elems) > 2:
for str in data.col1_startswith:
if line.lower().startswith(str):
valid_bed_data = True
break
if valid_bed_data:
if len(elems) < 6:
dataset.metadata.is_strandCol = "false"
dataset.metadata.strandCol = 0
else:
dataset.metadata.is_strandCol = "true"
dataset.metadata.strandCol = 6
break
if i == 30: break
if valid_bed_data:
Tabular.set_meta( self, dataset, i )
else:
dataset.metadata.is_strandCol = "false"
dataset.metadata.strandCol = 0
for i, col_type in enumerate(dataset.metadata.column_types):
#extra columns should be ok
if i >= len(bed_col_types): return
#invalid column type, this is no longer a bed file
if col_type not in bed_col_types[i]:
dataset.change_datatype('interval')
return
def as_ucsc_display_file( self, dataset, **kwd ):
"""Returns file contents with only the bed data. If bed 6+, treat as interval."""
for line in open(dataset.file_name):