EricR86
commented
10 years ago Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).
From epa...@uw.edu on September 12, 2012 17:25:11
It looks like this arises from Genomedata archives without a sequence. see https://code.google.com/p/segtools/issues/detail?id=31
Original report (archived issue) by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).
From Google Code Issue #18
Imported Labels: bug, imported, Priority-Medium
From epa...@uw.edu 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_0does not have a child namedseqI am using Genomedata 1.3.2
Original issue: http://code.google.com/p/genomedata/issues/detail?id=18