Genome object does not sufficiently process directory path

[EricR86]

From orion.bu...@gmail.com on January 04, 2010 19:17:22

Creating a Genome object from a path with a "~" causes
tracknames_continuous to fail when called on the Genome object, but not on
a child Chromosome object. This suggests the presented path argument is not
being processed by the Genome object, though it probably should be.

genome = Genome("/projects/segtools/data/genomedata.all")
genome["chr1"].tracknames_continuous
['BDP1.K562', 'BRF1.K562', 'cFos.GM12878', 'cFos.K562', 'cJun.K562',
'cMyc.K562.Iyer', 'cMyc.K562', 'CTCF.GM12878.Iyer',
'CTCF.GM12878.Bernstein', 'CTCF.GM12878.Stam', 'CTCF.K562.Bernstein',
'CTCF.K562.Iyer', 'CTCF.K562.Stam', 'DNaseI.GM12878.Crawford',
'DNaseI.GM12878.Stam', 'DNaseI.K562.Crawford', 'DNaseI.K562.Stam',
'E2F4.K562', 'E2F6.K562', 'Egr1.GM12878', 'Egr1.K562', 'FAIRE.GM12878',
'FAIRE.K562', 'GABP.GM12878', 'GABP.K562', 'GATA1.K562', 'H3K27ac.GM12878',
'H3K27ac.K562', 'H3K27me3.GM12878', 'H3K27me3.K562', 'H3K36me3.GM12878',
'H3K36me3.K562', 'H3K4me1.GM12878', 'H3K4me1.K562', 'H3K4me2.GM12878',
'H3K4me2.K562', 'H3K4me3.GM12878.Bernstein', 'H3K4me3.GM12878.Stam',
'H3K4me3.K562.Bernstein', 'H3K4me3.K562.Stam', 'H3K9ac.GM12878',
'H3K9ac.K562', 'H3K9me1.K562', 'H4K20me1.GM12878', 'H4K20me1.K562',
'JunD.GM12878', 'JunD.K562', 'Max.GM12878', 'Max.K562', 'NFE2.K562',
'NRSF.GM12878', 'NRSF.K562', 'Pol2b.K562', 'Pol2.GM12878.Myers',
'Pol2.GM12878.Snyder', 'Pol2.K562.Myers', 'Pol2.K562.Snyder',
'Pol3.GM12878', ' Rad21 .K562', 'RPC155.K562', 'SETDB1.K562',
'Sin3Ak20.GM12878', 'Sin3Ak20.K562', 'SIRT6.K562', 'SRF.GM12878',
'SRF.K562', 'TAFII.GM12878', 'TAFII.K562', 'TR4.K562', 'USF1.GM12878',
'Usf1.K562', 'XRCC4.K562', 'ZNF263.K562']
genome.tracknames_continuous
Traceback (most recent call last):
File "", line 1, in
File
"/net/noble/vol1/software/modules-sw/genomedata/1.0.0/Linux/RHEL4/x86_64/lib/python2.5/genomedata/init.py",
line 193, in tracknames_continuous
for chromosome in self:
File
"/net/noble/vol1/software/modules-sw/genomedata/1.0.0/Linux/RHEL4/x86_64/lib/python2.5/genomedata/init.py",
line 108, in iter
for filepath in sorted(self.dirpath.files("*" + SUFFIX)):
File
"/net/noble/vol1/software/modules-sw/python/2.5.4/Linux/RHEL4/x86_64/lib/python2.5/site-packages/path.py",
line 357, in files
return [p for p in self.listdir(pattern) if p.isfile()]
File
"/net/noble/vol1/software/modules-sw/python/2.5.4/Linux/RHEL4/x86_64/lib/python2.5/site-packages/path.py",
line 328, in listdir
names = os.listdir(self)
OSError: [Errno 2] No such file or directory:
'/projects/segtools/data/genomedata.all'
genome =
Genome("/net/noble/vol2/home/stasis/projects/segtools/data/genomedata.all")
genome.tracknames_continuous
['BDP1.K562', 'BRF1.K562', 'cFos.GM12878', 'cFos.K562', 'cJun.K562',
'cMyc.K562.Iyer', 'cMyc.K562', 'CTCF.GM12878.Iyer',
'CTCF.GM12878.Bernstein', 'CTCF.GM12878.Stam', 'CTCF.K562.Bernstein',
'CTCF.K562.Iyer', 'CTCF.K562.Stam', 'DNaseI.GM12878.Crawford',
'DNaseI.GM12878.Stam', 'DNaseI.K562.Crawford', 'DNaseI.K562.Stam',
'E2F4.K562', 'E2F6.K562', 'Egr1.GM12878', 'Egr1.K562', 'FAIRE.GM12878',
'FAIRE.K562', 'GABP.GM12878', 'GABP.K562', 'GATA1.K562', 'H3K27ac.GM12878',
'H3K27ac.K562', 'H3K27me3.GM12878', 'H3K27me3.K562', 'H3K36me3.GM12878',
'H3K36me3.K562', 'H3K4me1.GM12878', 'H3K4me1.K562', 'H3K4me2.GM12878',
'H3K4me2.K562', 'H3K4me3.GM12878.Bernstein', 'H3K4me3.GM12878.Stam',
'H3K4me3.K562.Bernstein', 'H3K4me3.K562.Stam', 'H3K9ac.GM12878',
'H3K9ac.K562', 'H3K9me1.K562', 'H4K20me1.GM12878', 'H4K20me1.K562',
'JunD.GM12878', 'JunD.K562', 'Max.GM12878', 'Max.K562', 'NFE2.K562',
'NRSF.GM12878', 'NRSF.K562', 'Pol2b.K562', 'Pol2.GM12878.Myers',
'Pol2.GM12878.Snyder', 'Pol2.K562.Myers', 'Pol2.K562.Snyder',
'Pol3.GM12878', ' Rad21 .K562', 'RPC155.K562', 'SETDB1.K562',
'Sin3Ak20.GM12878', 'Sin3Ak20.K562', 'SIRT6.K562', 'SRF.GM12878',
'SRF.K562', 'TAFII.GM12878', 'TAFII.K562', 'TR4.K562', 'USF1.GM12878',
'Usf1.K562', 'XRCC4.K562', 'ZNF263.K562']

Original issue: http://code.google.com/p/genomedata/issues/detail?id=5

[EricR86]

From orion.bu...@gmail.com on February 11, 2010 16:53:32

This is getting annoying, so I'm increasing the priority

Labels: -Priority-Low Priority-Medium

[EricR86]

From orion.bu...@gmail.com on February 12, 2010 17:11:04

This is now fixed.

Status: Fixed

[EricR86]

From orion.bu...@gmail.com on February 12, 2010 17:25:07

Also added check upon creation for existence of file/directory so Genomedata reliably
raises an IOError if the path is not valid.