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Bug fixes, enhancements (including a new test) for the aggregate_binned_scores_in_intervals tool and added new code file for handling tool exceptions.

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This commit is contained in:
Greg Von Kuster
2007-09-19 19:45:28 +00:00
parent 23fd74c2c5
commit 20126a37a4
3 changed files with 70 additions and 53 deletions
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lib/galaxy/tools/exception_handling.py
+30
View File
@@ -0,0 +1,30 @@
"""
Exceptions and handlers for tools
"""
class UCSCLimitException( Exception ):
pass
class UCSCOutWrapper( object ):
"""File-like object that throws an exception if it encounters the UCSC limit error lines"""
def __init__( self, other ):
self.other = iter( other )
# Need one line of lookahead to be sure we are hitting the limit message
self.lookahead = None
def __iter__( self ):
return self
def __next__( self ):
if self.lookahead is None:
line = self.other.next()
else:
line = self.lookahead
self.lookahead = None
if line.startswith( "----------" ):
next_line = self.other.next()
if next_line.startswith( "Reached output limit" ):
raise UCSCLimitException( next_line.strip() )
else:
self.lookahead = next_line
return line
def readline(self):
return self.__next__()
tools/stats/aggregate_binned_scores_in_intervals.xml
+5
View File
@@ -20,6 +20,11 @@
<param name="datasets" value="/depot/data2/galaxy/binned_scores/hg17/phastcons_encode_sep2005_tba" />
<output name="out_file1" file="aggregate_binned_scores_in_intervals.out" />
</test>
<test>
<param name="input1" value="9_hg18.bed" dbkey="hg18" ftype="bed"/>
<param name="datasets" value="/depot/data2/galaxy/binned_scores/hg18/phastCons17way/ba" />
<output name="out_file1" file="aggregate_binned_scores_in_intervals2.out" />
</test>
</tests>
<help>
tools/stats/aggregate_scores_in_intervals.py
+35 -53
View File
@@ -25,6 +25,7 @@ from bx.bitset import *
from bx.bitset_builders import *
from fpconst import isNaN
from bx.cookbook import doc_optparse
from galaxy.tools.exception_handling import *
class FileBinnedArrayDir( DictMixin ):
"""
@@ -47,39 +48,6 @@ class FileBinnedArrayDir( DictMixin ):
raise KeyError( "File does not exist: " + fname )
return value
"""
TODO: move the following 2 classes to a better location so that other tools can take advantage of them.
Talk to Ian about possibly moving them to the bx egg.
"""
class UCSCLimitException( Exception ):
pass
class UCSCOutWrapper( object ):
"""
File-like object that throws an exception if it encounters the UCSC limit error lines
"""
def __init__( self, other ):
self.other = iter( other )
# Need one line of lookahead to be sure we are hitting the limit message
self.lookahead = None
def __iter__( self ):
return self
def __next__( self ):
if self.lookahead is None:
line = self.other.next()
else:
line = self.lookahead
self.lookahead = None
if line.startswith( "----------" ):
next_line = self.other.next()
if next_line.startswith( "Reached output limit" ):
raise UCSCLimitException( next_line.strip() )
else:
self.lookahead = next_line
return line
def readline(self):
return self.__next__()
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
@@ -132,7 +100,7 @@ def main():
doc_optparse.exit()
if score_fname == 'None':
print 'Invalid genome build - this tool currently only works with data from genome builds hg16, hg17 or hg18. Click "edit attributes" (the pencil icon) in your history item to correct the genome build if appropriate.'
print 'This tool works with data from genome builds hg16, hg17 or hg18. Click the pencil icon in your history item to set the genome build if appropriate.'
sys.exit()
try:
@@ -140,11 +108,11 @@ def main():
start_col = int(start_col) - 1
stop_col = int(stop_col) - 1
except:
print 'Invalid column number for chrom, start or end column, chrom: %s start: %s end: %s' %(chrom_col, start_col, stop_col)
print 'Chrom, start & end column not properly set, click the pencil icon in your history item to set these values.'
sys.exit()
if chrom_col < 0 or start_col < 0 or stop_col < 0:
print 'Invalid column number for chrom, start or end column, chrom: %s start: %s end: %s' %(chrom_col, start_col, stop_col)
print 'Chrom, start & end column not properly set, click the pencil icon in your history item to set these values.'
sys.exit()
if binned:
@@ -159,32 +127,46 @@ def main():
skipped_lines = 0
first_invalid_line = 0
invalid_line = None
invalid_line = ''
for i, line in enumerate( open( interval_fname )):
line = line.strip()
if line and line != '' and not line.startswith( '#' ):
valid = True
line = line.rstrip('\r\n')
if line and not line.startswith( '#' ):
fields = line.split()
try:
chrom, start, stop = fields[chrom_col], int( fields[start_col] ), int( fields[stop_col] )
chrom, start, stop = fields[chrom_col], int( fields[start_col] ), int( fields[stop_col] )
except:
valid = False
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
if valid:
total = 0
count = 0
min_score = 100000000
max_score = -100000000
for j in range( start, stop ):
if chrom in scores_by_chrom and scores_by_chrom[chrom][j]:
# Skip if base is masked
if masks and chrom in masks:
if masks[chrom][j]:
continue
# Get the score, only count if not 'nan'
score = scores_by_chrom[chrom][j]
if not isNaN( score ):
total += score
count += 1
max_score = max( score, max_score )
min_score = min( score, min_score )
valid2 = True
if chrom in scores_by_chrom:
try:
scores_by_chrom[chrom][j]
except:
valid2 = False
if valid2:
# Skip if base is masked
if masks and chrom in masks:
if masks[chrom][j]:
continue
# Get the score, only count if not 'nan'
score = scores_by_chrom[chrom][j]
if not isNaN( score ):
total += score
count += 1
max_score = max( score, max_score )
min_score = min( score, min_score )
if count > 0:
avg = total/count
else:
@@ -201,7 +183,7 @@ def main():
out_line.append(max_score)
print >> out_file, "\t".join( map( str, out_line ) )
except:
else:
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1