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Update GenomicIntervalReader using tools to use NiceReaderWrapper.

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Bad lines are silently ignored.
This commit is contained in:
Daniel Blankenberg
2007-08-03 15:18:24 +00:00
parent b22fecf1d3
commit 868c5a26b2
8 changed files with 10 additions and 10 deletions
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tools/encode/random_intervals_no_bits.py
+3 -3
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@@ -104,12 +104,12 @@ def main():
#set up bounding regions to hold random intervals
bounds = []
for bound in bx.intervals.io.GenomicIntervalReader( open( region_fname, 'r' ), chrom_col=0, start_col=1, end_col=2, fix_strand=True): bounds.append(bound)
for bound in bx.intervals.io.NiceReaderWrapper( open( region_fname, 'r' ), chrom_col=0, start_col=1, end_col=2, fix_strand=True): bounds.append(bound)
#set up length and number of regions to mimic
regions = [ [] for i in range(len(bounds)) ]
for region in bx.intervals.io.GenomicIntervalReader( open(intervals_fname, 'r' ), chrom_col=interval_chr, start_col=interval_start, end_col=interval_end, strand_col=interval_strand, fix_strand=True, return_header=False):
for region in bx.intervals.io.NiceReaderWrapper( open(intervals_fname, 'r' ), chrom_col=interval_chr, start_col=interval_start, end_col=interval_end, strand_col=interval_strand, fix_strand=True, return_header=False):
#loop through bounds, find first proper bounds then add
#if an interval crosses bounds, it will be added to the first bound
for i in range(len(bounds)):
@@ -127,7 +127,7 @@ def main():
#read mask file
mask = []
if use_mask != "no_mask":
for region in bx.intervals.io.GenomicIntervalReader( open(mask_fname, 'r' ), chrom_col=mask_chr, start_col=mask_start, end_col=mask_end, fix_strand=True): mask.append(region)
for region in bx.intervals.io.NiceReaderWrapper( open(mask_fname, 'r' ), chrom_col=mask_chr, start_col=mask_start, end_col=mask_end, fix_strand=True): mask.append(region)
out_file = open (out_fname, "w") or die ("Can not open output file")