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Fixes and enhancements for displaying interval/bed files at UCSC.

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This commit is contained in:
Daniel Blankenberg
2007-11-08 20:14:20 +00:00
parent 69ddb7d83f
commit 29c9521010
1 changed files with 14 additions and 6 deletions
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lib/galaxy/datatypes/interval.py
+14 -6
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@@ -99,8 +99,8 @@ class Interval( Tabular ):
"""Return a chrom, start, stop tuple for viewing a file."""
if dataset.has_data() and dataset.state == dataset.states.OK:
try:
c, s, e, t = dataset.metadata.chromCol, dataset.metadata.startCol, dataset.metadata.endCol, dataset.metadata.strandCol
c, s, e, t = int(c)-1, int(s)-1, int(e)-1, int(t)-1
c, s, e = dataset.metadata.chromCol, dataset.metadata.startCol, dataset.metadata.endCol
c, s, e = int(c)-1, int(s)-1, int(e)-1
peek = []
for idx, line in enumerate(file(dataset.file_name)):
@@ -125,13 +125,21 @@ class Interval( Tabular ):
def as_ucsc_display_file( self, dataset, **kwd ):
"""Returns file contents with only the bed data"""
fd, temp_name = tempfile.mkstemp()
c, s, e, t = dataset.metadata.chromCol, dataset.metadata.startCol, dataset.metadata.endCol, dataset.metadata.strandCol
c, s, e, t = int(c)-1, int(s)-1, int(e)-1, int(t)-1
c, s, e, t, n = dataset.metadata.chromCol, dataset.metadata.startCol, dataset.metadata.endCol, dataset.metadata.strandCol or 0, dataset.metadata.nameCol or 0
c, s, e, t, n = int(c)-1, int(s)-1, int(e)-1, int(t)-1, int(n)-1
if t >= 0: # strand column (should) exists
for elems in util.file_iter(dataset.file_name):
for i, elems in enumerate( util.file_iter(dataset.file_name) ):
strand = "+"
name = "region_%i" % i
if n >= 0 and n < len( elems ): name = elems[n]
if t<len(elems): strand = elems[t]
tmp = [ elems[c], elems[s], elems[e], '1', '2', strand ]
tmp = [ elems[c], elems[s], elems[e], name, '0', strand ]
os.write(fd, '%s\n' % '\t'.join(tmp) )
elif n >= 0: # name column (should) exists
for i, elems in enumerate( util.file_iter(dataset.file_name) ):
name = "region_%i" % i
if n >= 0 and n < len( elems ): name = elems[n]
tmp = [ elems[c], elems[s], elems[e], name ]
os.write(fd, '%s\n' % '\t'.join(tmp) )
else:
for elems in util.file_iter(dataset.file_name):