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Merge pull request #851 from ged-lab/fix/sandbox_scripts
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fix sandbox scripts for kfile changes
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mr-c committed Mar 6, 2015
2 parents c22aaa3 + aa98000 commit 9970094
Showing 3 changed files with 10 additions and 5 deletions.
5 changes: 5 additions & 0 deletions ChangeLog
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
2015-03-06 Titus Brown <titus@idyll.org>

* sandbox/{collect-reads.py,saturate-by-median.py}: update for 'force'
argument in khmer.kfile functions, so that khmer-recipes compile.

2015-03-02 Titus Brown <titus@idyll.org>

* sandbox/{combine-pe.py,compare-partitions.py,count-within-radius.py,
6 changes: 3 additions & 3 deletions sandbox/collect-reads.py
Original file line number Diff line number Diff line change
@@ -71,10 +71,10 @@ def main():
filenames = args.input_sequence_filename

for name in args.input_sequence_filename:
check_file_status(name)
check_file_status(name, False)

check_space(args.input_sequence_filename)
check_space_for_hashtable(args.n_tables * args.min_tablesize)
check_space(args.input_sequence_filename, False)
check_space_for_hashtable(args.n_tables * args.min_tablesize, False)

print 'Saving k-mer counting table to %s' % base
print 'Loading sequences from %s' % repr(filenames)
4 changes: 2 additions & 2 deletions sandbox/saturate-by-median.py
Original file line number Diff line number Diff line change
@@ -185,9 +185,9 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
report_frequency = args.report_frequency

check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames)
check_space(args.input_filenames, False)
if args.savetable:
check_space_for_hashtable(args.n_tables * args.min_tablesize)
check_space_for_hashtable(args.n_tables * args.min_tablesize, False)

# list to save error files along with throwing exceptions
if args.force:

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