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From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Wed, 8 Nov 2017 15:35:02 -0500
Subject: [PATCH] address #227
---
pybedtools/contrib/bigwig.py | 62 +++++++++++++++++++++++++++++++++++++-------
pybedtools/test/test1.py | 36 ++++++++++++++-----------
2 files changed, 73 insertions(+), 25 deletions(-)
--- a/pybedtools/contrib/bigwig.py
+++ b/pybedtools/contrib/bigwig.py
@@ -48,8 +48,17 @@ def bedgraph_to_bigwig(bedgraph, genome,
bedgraph.fn,
genome_file,
output]
- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- stdout, stderr = p.communicate()
+ try:
+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout, stderr = p.communicate()
+ except FileNotFoundError:
+ raise FileNotFoundError(
+ "bedGraphToBigWig was not found on the path. This is an external "
+ "tool from UCSC which can be downloaded from "
+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
+ "`conda install ucsc-bedgraphtobigwig`"
+ )
+
if p.returncode:
raise ValueError("cmds: %s\nstderr:%s\nstdout:%s"
% (" ".join(cmds), stderr, stdout))
@@ -72,8 +81,16 @@ def bigwig_to_bedgraph(fn, chrom=None, s
outfn = pybedtools.BedTool._tmp()
cmds.append(outfn)
- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- stdout, stderr = p.communicate()
+ try:
+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout, stderr = p.communicate()
+ except FileNotFoundError:
+ raise FileNotFoundError(
+ "bigWigToBedGraph was not found on the path. This is an external "
+ "tool from UCSC which can be downloaded from "
+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
+ "`conda install ucsc-bedgraphtobigwig`"
+ )
if p.returncode:
raise ValueError("cmds: %s\nstderr:%s\nstdout:%s"
% (" ".join(cmds), stderr, stdout))
@@ -87,8 +104,17 @@ def wig_to_bigwig(wig, genome, output):
wig.fn,
genome_file,
output]
- subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- stdout, stderr = p.communicate()
+
+ try:
+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout, stderr = p.communicate()
+ except FileNotFoundError:
+ raise FileNotFoundError(
+ "bigWigToBedGraph was not found on the path. This is an external "
+ "tool from UCSC which can be downloaded from "
+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
+ "`conda install ucsc-bedgraphtobigwig`"
+ )
if p.returncode:
raise ValueError('cmds: %s\nstderr:%s\nstdout:%s'
% (' '.join(cmds), stderr, stdout))
@@ -120,15 +146,31 @@ def bam_to_bigwig(bam, genome, output, s
x.fn,
genome_file,
output]
- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
- stdout, stderr = p.communicate()
+ try:
+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
+ stdout, stderr = p.communicate()
+ except FileNotFoundError:
+ raise FileNotFoundError(
+ "bedGraphToBigWig was not found on the path. This is an external "
+ "tool from UCSC which can be downloaded from "
+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
+ "`conda install ucsc-bedgraphtobigwig`"
+ )
if p.returncode and 'bedSort' in stderr:
print('BAM header was not sorted; sorting bedGraph')
y = x.sort()
cmds[1] = y.fn
- p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
- stdout, stderr = p.communicate()
+ try:
+ p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
+ stdout, stderr = p.communicate()
+ except FileNotFoundError:
+ raise FileNotFoundError(
+ "bedSort was not found on the path. This is an external "
+ "tool from UCSC which can be downloaded from "
+ "http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use "
+ "`conda install ucsc-bedgraphtobigwig`"
+ )
if p.returncode:
raise ValueError('cmds: %s\nstderr: %s\nstdout: %s'
--- a/pybedtools/test/test1.py
+++ b/pybedtools/test/test1.py
@@ -2104,21 +2104,27 @@ def test_issue_196():
def test_issue_178():
- fn = pybedtools.example_filename('gdc.othersort.bam')
- pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')
- x = pybedtools.contrib.bigwig.bigwig_to_bedgraph('tmp.bw')
- assert x == fix(
- '''
- chr2L 70 75 1
- chr2L 140 145 1
- chr2L 150 155 1
- chr2L 160 165 1
- chr2L 210 215 1
- chrX 10 15 1
- chrX 70 75 1
- chrX 140 145 1
- ''')
- os.unlink('tmp.bw')
+ try:
+ fn = pybedtools.example_filename('gdc.othersort.bam')
+ pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')
+ x = pybedtools.contrib.bigwig.bigwig_to_bedgraph('tmp.bw')
+ assert x == fix(
+ '''
+ chr2L 70 75 1
+ chr2L 140 145 1
+ chr2L 150 155 1
+ chr2L 160 165 1
+ chr2L 210 215 1
+ chrX 10 15 1
+ chrX 70 75 1
+ chrX 140 145 1
+ ''')
+ os.unlink('tmp.bw')
+
+ # If bedGraphToBigWig is not on the path, see
+ # https://github.com/daler/pybedtools/issues/227
+ except FileNotFoundError:
+ pass
def test_issue_203():
x = pybedtools.example_bedtool('x.bed')
|
