From: Ryan Dale 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')