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From [email protected] on November 16, 2010 11:34:40

Use the drmaa module if available.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=16

From [email protected] on March 16, 2010 17:09:50

The wiggle parsing code in genomedata_load_data.c assumes the wiggle file
will start with variableStep or fixedStep. The wiggle spec states that the
first line must be a track definition line. If a standard wiggle file is
presented, the loader will default to reading it in BED format and throw a
large number of errors.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=14

From [email protected] on January 26, 2010 18:01:20

Right now, Chromosome.supercontigs[5] returns a list of all supercontigs,
if any, that overlap base position 5.

It would be useful to have something that returns a list of supercontigs,
instead of just providing the ability to iterate over them.
Chromosome.supercontigs seems like an obvious solution, but this conflicts
with the existing function. Perhaps one of them should be
Chromosome.supercontigs(...), but this is such a small distinction it is
likely to result it many errors.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=8

From [email protected] on May 27, 2010 14:16:52

Users should be allowed to create Genomedata archives without any data
tracks (just sequence)

The following sequence should work:
$ genomedata-load-seq genomedata.test chr*.fa.gz
$ genomedata-close-data genomedata.test

As of now, it crashes:

Traceback (most recent call last):
File "genomedata-close-data",
line 8, in
load_entry_point('genomedata==1.1.1', 'console_scripts',
'genomedata-close-data')()
File "genomedata-1.1.1-py2.6.egg/genomedata/_close_data.py",
line 166, in main
return close_data(gdfilename, **kwargs)
File "genomedata-1.1.1-py2.6.egg/genomedata/_close_data.py",
line 139, in close_data
write_metadata(chromosome, verbose=verbose)
File "genomedata-1.1.1-py2.6.egg/genomedata/_close_data.py",
line 30, in write_metadata
tracknames = chromosome.tracknames_continuous
File "genomedata-1.1.1-py2.6.egg/genomedata/init.py",
line 766, in tracknames_continuous
return self.h5file.root._v_attrs.tracknames.tolist()
File "tables-2.1.2-py2.6-macosx-10.6-universal.egg/tables/attributeset.py",
line 300, in getattr
(name, self._v__nodePath)
AttributeError: Attribute 'tracknames' does not exist in node: '/'

A hack to essentially allow this without increasing the size of the archive
(or taking any time to load a track) would be to create an empty track
before closing with the following:
$ genomedata-load-seq genomedata.test chr*.fa.gz
$ genomedata-open-data default
$ genomedata-close-data genomedata.test

Original issue: http://code.google.com/p/genomedata/issues/detail?id=15

From [email protected] on February 24, 2010 18:05:14

Currently, if a Genomedata archive is opened with mode="r+" in Python,
genomedata-close-data must be called on the archive from the shell before
it can be re-opened in Python.

Additionally, the dirty bit is set on all chromosomes opened from a
mode="r+" Genome object, regardless if they are changed or not (i.e. all
are opened with mode="r+" when calling Genome.tracknames_continuous).

Original issue: http://code.google.com/p/genomedata/issues/detail?id=12

From [email protected] on February 24, 2010 17:59:50

A usefule feature in the future would be a command that would combine a
directory Genomedata archive into a single-file archive, if this could be
done quickly and easily. This would then allow the archive to be distributed
directly, without creating a tarball.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=11

From jay.hesselberth on June 16, 2011 15:10:06

I have multiple discontiguous coords on a chromosome that I want get data for, and I'd like to do it without looping over them.

I can do this with numpy:

temp = numpy.array([1,2,3,4,5])
coords = [1,3]
temp[coords]
array([2, 4])

but I can't seem to do the same thing with genomedata, e.g.

genome[chrom][coords,trackname] doesn't work.

Am I stuck looping?

Original issue: http://code.google.com/p/genomedata/issues/detail?id=17

From [email protected] on December 15, 2009 16:59:28

What steps will reproduce the problem? 1. Took standard genomedata.round5a.tier1 collection (created before update
to genomedata-close-data, so there are supercontigs without continuous
children.
2. Used genomedata-erase-track to remove the two DNaseI.*.Crawford tracks.
3. Replaced the data in parallel using genomedata-load-data.
4. Used genomedata-close-data to recompute the metadata for the new track.

This should succeed, making the genomedata collection usable with the new
data. Instead, just near the end of genomedata-close-data, the following
exceptions was raised:

writing metadata for chr1
scanning supercontig_0
BDP1.K562
BRF1.K562
cFos.GM12878
cFos.K562
cJun.K562
cMyc.K562.Iyer
cMyc.K562
CTCF.GM12878.Iyer
CTCF.GM12878
CTCF.GM12878.Stam
CTCF.K562.Bernstein
CTCF.K562.Iyer
CTCF.K562.Stam
DNaseI.GM12878.Crawford
HDF5-DIAG: Error detected in HDF5 (1.8.2) thread 0:
#000: H5Dio.c line 175 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#1: H5Dio.c line 407 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#2: H5Dchunk.c line 1517 in H5D_chunk_read(): unable to read raw data chunk
major: Low-level I/O
minor: Read failed
#3: H5Dchunk.c line 2443 in H5D_chunk_lock(): data pipeline read failed
major: Data filters
minor: Filter operation failed
#4: H5Z.c line 1008 in H5Z_pipeline(): filter returned failure during read
major: Data filters
minor: Read failed
#5: H5Zdeflate.c line 117 in H5Z_filter_deflate(): inflate() failed
major: Data filters
minor: Unable to initialize object
Traceback (most recent call last):
File
"/net/noble/vol2/home/stasis/arch/Linux/RHEL4/x86_64/bin/genomedata-close-data",
line 8, in
load_entry_point('genomedata==0.1.7.dev- r2670 ', 'console_scripts',
'genomedata-close-data')()
File
"/net/noble/vol2/home/stasis/arch/Linux/RHEL4/x86_64/lib/python2.5/genomedata-0.1.7.dev_r2670-py2.5.egg/genomedata/_close_data.py",
line 164, in main
return close_data(genomedatadir, **kwargs)
File
"/net/noble/vol2/home/stasis/arch/Linux/RHEL4/x86_64/lib/python2.5/genomedata-0.1.7.dev_r2670-py2.5.egg/genomedata/_close_data.py",
line 140, in close_data
write_metadata(chromosome, verbose=verbose)
File
"/net/noble/vol2/home/stasis/arch/Linux/RHEL4/x86_64/lib/python2.5/genomedata-0.1.7.dev_r2670-py2.5.egg/genomedata/_close_data.py",
line 74, in write_metadata
col = continuous[:, col_index]
File
"/net/gs/vol3/software/modules-sw/python/2.5.4/Linux/RHEL4/x86_64/lib/python2.5/site-packages/tables/array.py",
line 504, in getitem
arr = self._readSlice(startl, stopl, stepl, shape)
File
"/net/gs/vol3/software/modules-sw/python/2.5.4/Linux/RHEL4/x86_64/lib/python2.5/site-packages/tables/array.py",
line 571, in _readSlice
self._g_readSlice(startl, stopl, stepl, arr)
File "hdf5Extension.pyx", line 1057, in
tables.hdf5Extension.Array._g_readSlice
tables.exceptions.HDF5ExtError: Problems reading the array data.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=4

From [email protected] on November 10, 2009 18:14:53

This would allow people to get started more quickly when they don't need
the sequence. One place to get the parameters of the genome from would be
the AGP of the assembly (for example,
< ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/AGP/> ).
Another would be a simple list of the size of each chromosome. This would
result in the creation of chromosomes with only one supercontig.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=2

From [email protected] on January 26, 2010 18:05:13

When loading the sequence, it would be useful to store a sequence length
attribute so Chromosome objects know their length. This would allow full
slicing and provide a more straightforward behavior for Chromosome slicing.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=9

From [email protected] on September 12, 2012 19:03:07

If I run the following python code

import genomedata
genome = genomedata.Genome(path_to_archive)
chr1 = genome["chr1"]
chr1.seq[chr1.start:chr1.end]

I get the error

/net/noble/vol1/software/modules-sw/genomedata/1.3.2/Linux/RHEL5/x86_64/lib/python2.7/genomedata/init.py:1174: UserWarning: slice of chromosome sequence spans more than one supercontig (filling gaps with 'NaN')
warn("slice of chromosome sequence spans more than one supercontig"
Traceback (most recent call last):
File "", line 1, in
File "/net/noble/vol1/software/modules-sw/genomedata/1.3.2/Linux/RHEL5/x86_64/lib/python2.7/genomedata/init.py", line 1197, in getitem
seq[dest_start:dest_end] = supercontig.seq[sc_start:sc_end]
File "/net/noble/vol1/software/modules-sw/genomedata/1.3.2/Linux/RHEL5/x86_64/lib/python2.7/genomedata/init.py", line 1136, in seq
return self.h5group.seq
File "/net/gs/vol3/software/modules-sw/python/2.7/Linux/RHEL5/x86_64/lib/python2.7/site-packages/tables/group.py", line 834, in getattr
return self._f_getChild(name)
File "/net/gs/vol3/software/modules-sw/python/2.7/Linux/RHEL5/x86_64/lib/python2.7/site-packages/tables/group.py", line 705, in _f_getChild
self._g_checkHasChild(childname)
File "/net/gs/vol3/software/modules-sw/python/2.7/Linux/RHEL5/x86_64/lib/python2.7/site-packages/tables/group.py", line 446, in _g_checkHasChild
% (self._v_pathname, name))
tables.exceptions.NoSuchNodeError: group /supercontig_0 does not have a child named seq

I am using Genomedata 1.3.2

Original issue: http://code.google.com/p/genomedata/issues/detail?id=18

From [email protected] 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

From jay.hesselberth on February 10, 2010 17:35:05

What steps will reproduce the problem? 1. Launce instance of ami-0f30d166 on EC2
2. wget genomedata install script
3. python install.py

...

During genomedata build get the error:

easy_install genomedata genomedata>=1.0.1
Searching for genomedata
Reading http://pypi.python.org/simple/genomedata/ Reading http://noble.gs.washington.edu/proj/genomedata/ Reading http://noble.gs.washington.edu/~mmh1/software/genomedata/ Best match: genomedata 1.0.1
Downloading http://noble.gs.washington.edu/proj/genomedata/genomedata-1.0.1.tar.gz Processing genomedata-1.0.1.tar.gz
Running genomedata-1.0.1/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-tbRhGC/genomedata-1.0.1/egg-dist-tmp-5_muDq

src/genomedata_load_data.c: In function ‘fatal’:
src/genomedata_load_data.c:93: warning: format not a string literal and no
format arguments
/usr/include/bits/error.h: In function ‘error_at_line’:
/usr/include/bits/error.h:72: error: invalid use of ‘__builtin_va_arg_pack ()’
/usr/include/bits/error.h: In function ‘error’:
/usr/include/bits/error.h:43: error: invalid use of ‘__builtin_va_arg_pack ()’
error: Setup script exited with error: command 'gcc' failed with exit status 1
Error occured installing genomedata What version of the product are you using? On what operating system? genomedata 1.0.1 on Ubuntu 9.04 Please provide any additional information below. genomedata installs find under Fedora. Assuming this has something to do
with comment on line 93 of genomedata_load_seq.c

/* XXX: GNU-only extension; should be wrapped */

Original issue: http://code.google.com/p/genomedata/issues/detail?id=10

From [email protected] on March 16, 2010 16:18:59

Genomedata seems to work except for load data on Mac OS X.

This is because of incompatibilities in error.h, which could potentially be
solved by switching to Gnulib.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=13

From [email protected] on January 08, 2010 23:24:11

I have no idea why this is happening, but if
Chromosome.tracknames_continuous is called before accessing any data,
python segfaults when a data access is attempted. If, however, data is
accessed first, everything is fine:

Accessing data first:
[stasis@n001 0107-signal-dist-speedup]$ python
Python 2.5.4 ( r254 :67916, Jan 8 2009, 14:27:04)
[GCC 3.4.6 20060404 (Red Hat 3.4.6-9)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

from genomedata import Genome
genome = Genome("../../data/genomedata.latest")
chr = genome["chr1"]
y = chr[100:1000]
x = genome.tracknames_continuous
y = chr[100:1000]

Calling tracknames_continuous first:
[stasis@n001 0107-signal-dist-speedup]$ python
Python 2.5.4 ( r254 :67916, Jan 8 2009, 14:27:04)
[GCC 3.4.6 20060404 (Red Hat 3.4.6-9)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

from genomedata import Genome
genome = Genome("../../data/genomedata.latest")
chr = genome["chr1"]
x = genome.tracknames_continuous
y = chr[100:1000]
Segmentation fault

Original issue: http://code.google.com/p/genomedata/issues/detail?id=6

From [email protected] on January 26, 2010 17:58:42

Something like:

with Genome(...) as genome:
genome.chromosomes

Since right now, if you just want the first chromosome, you have to do this:
with Genome(...) as genome:
for chromosome in genome:
break

Original issue: http://code.google.com/p/genomedata/issues/detail?id=7

From [email protected] on November 24, 2009 14:55:05

1. replace all data for a track with NaN
2. set the dirty flag

This will allow the easy replacement of the data with a new version.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=3

From [email protected] on March 06, 2013 03:41:17

What steps will reproduce the problem? 1.genomedata-load-data genomedata.test low < signal_low.wigFix What is the expected output? What do you see instead? I expect the wig data being loaded to my genomedata archive, but I got the following:

Warning! _HDF5 library version mismatched error_
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.5, library is 1.8.4
-------------- What version of the product are you using? On what operating system? I am using version 1.3.2 which was built on 1.8.4-patch1 on Ubuntu 12.10 with SGE cluster setup. Please provide any additional information below. I do not know how to set up this HDF5_DISABLE_VERSION_CHECK varible. It will be great if someone could show me how to do it.

Thanks.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=19

From [email protected] on November 10, 2009 18:06:57

Can copy what is done in Segway.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=1