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Issues 190 and 113 #213

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merged 3 commits into from
May 9, 2017
Merged

Issues 190 and 113 #213

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e83c621
docs on genome_cov warning about non-BED format
daler May 9, 2017
77abe75
address #190
daler May 9, 2017
1f6e216
Merge branch 'master' of github.com:daler/pybedtools
daler May 9, 2017
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20 changes: 18 additions & 2 deletions pybedtools/bedtool.py
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Original file line number Diff line number Diff line change
Expand Up @@ -603,7 +603,7 @@ def truncate_to_chrom(self, genome):

def tabix_intervals(self, interval_or_string):
"""
Retrieve all intervals within cooridnates from a "tabixed" BedTool.
Retrieve all intervals within coordinates from a "tabixed" BedTool.

Given either a string in "chrom:start-stop" format, or an interval-like
object with chrom, start, stop attributes, return a *streaming* BedTool
Expand Down Expand Up @@ -644,7 +644,11 @@ def tabix_intervals(self, interval_or_string):
def gen():
for i in results:
yield i + '\n'
return BedTool(gen())

# xref #190
x = BedTool(gen()).saveas()
tbx.close()
return x

def tabix(self, in_place=True, force=False, is_sorted=False):
"""
Expand Down Expand Up @@ -1991,6 +1995,14 @@ def genome_coverage(self):
"""
Wraps `bedtools genomecov`.

Note that some invocations of `bedtools genomecov` do not result in
a properly-formatted BED file. For example, the default behavior is to
report a histogram of coverage. Iterating over the resulting,
non-BED-format file will raise exceptions in pybedtools' parser.

Consider using the `BedTool.to_dataframe` method to convert these
non-BED files into a pandas DataFrame for further use.

Example usage:

BAM file input does not require a genome:
Expand All @@ -2011,6 +2023,10 @@ def genome_coverage(self):
chr2L 10212 10248 1
chr2L 10255 10291 1

Non-BED format results:
>>> a = pybedtools.example_bedtool('x.bed')
>>> b = a.genome_coverage(genome='dm3')
>>> df = b.to_dataframe(names=['chrom', 'depth', 'n', 'chromsize', 'fraction'])


"""
Expand Down