segtools-signal-distribution test_mod_identifydir/segway.0.bed test/chr1.genomedata
INFO:Note: NumExpr detected 36 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
INFO:NumExpr defaulting to 8 threads.
INFO:Loading Segmentation from file: test_mod_identifydir/segway.0.bed
INFO: Parsing lines from bed format
INFO:Loading finished in 121.5 seconds.
INFO:Generating signal distribution histograms
Traceback (most recent call last):
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/bin/segtools-signal-distribution", line 10, in <module>
sys.exit(main())
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 390, in main
validate(bedfilename, genomedatadir, outdir, **kwargs)
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 281, in validate
verbose=verbose)
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 99, in from_segmentation
for chromosome in chromosomes:
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 169, in __iter__
yield self[groupname]
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 203, in __getitem__
res = Chromosome(self.h5file, where="/" + name)
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 558, in __init__
if attrs.dirty:
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/tables/attributeset.py", line 305, in __getattr__
"'%s'" % (name, self._v__nodepath))
AttributeError: Attribute 'dirty' does not exist in node: '/supercontig_0'
with
statement if you want to do a quick check.segtools-signal-distribution -c chr1 test_mod_identifydir/segway.0.bed test/chr1.genomedata
INFO:Note: NumExpr detected 36 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
INFO:NumExpr defaulting to 8 threads.
INFO:Loading Segmentation from file: test_mod_identifydir/segway.0.bed
INFO: Parsing lines from bed format
INFO:Loading finished in 121.7 seconds.
INFO:Generating signal distribution histograms
['chr1']
Genome('test/chr1.genomedata')
Traceback (most recent call last):
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/bin/segtools-signal-distribution", line 10, in <module>
sys.exit(main())
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 390, in main
validate(bedfilename, genomedatadir, outdir, **kwargs)
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 281, in validate
verbose=verbose)
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 95, in from_segmentation
chromosomes = [genome[chrom] for chrom in chroms]
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 209, in __getitem__
raise KeyError("Could not find chromosome: %s" % name)
KeyError: 'Could not find chromosome: chr1'
segtools-signal-distribution test_mod_identifydir/segway.0.bed test/chr1.genomedata
INFO:Note: NumExpr detected 36 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
INFO:NumExpr defaulting to 8 threads.
INFO:Loading Segmentation from file: test_mod_identifydir/segway.0.bed
INFO: Parsing lines from bed format
INFO:Loading finished in 121.5 seconds.
INFO:Generating signal distribution histograms
Traceback (most recent call last):
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/bin/segtools-signal-distribution", line 10, in <module>
sys.exit(main())
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 390, in main
validate(bedfilename, genomedatadir, outdir, **kwargs)
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 281, in validate
verbose=verbose)
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 99, in from_segmentation
for chromosome in chromosomes:
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 169, in __iter__
yield self[groupname]
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 203, in __getitem__
res = Chromosome(self.h5file, where="/" + name)
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 558, in __init__
if attrs.dirty:
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/tables/attributeset.py", line 305, in __getattr__
"'%s'" % (name, self._v__nodepath))
AttributeError: Attribute 'dirty' does not exist in node: '/supercontig_0'
>>> from genomedata import Genome
>>> gdfilename = "/net/noble/vol3/user/karolb/results/ranz0/process2segway/test"
>>> with Genome(gdfilename) as genome:
... chromosome = genome["chr19"]
>>> chromosome
<Chromosome 'chr19', file='/net/noble/vol3/user/karolb/results/ranz0/process2segway/test/chr19.genomedata'>
>>> data = chromosome[10000:10050, 0:3]
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py3.6/lib/python3.6/site-packages/genomedata/__init__.py", line 713, in __getitem__
assert self.isopen
AssertionError
chr1 3000000 85347103 0 1000 . 3000000 85347103 27,158,119 69855
chr1 3000000 85347103 1 1000 . 3000000 85347103 217,95,2 36054
chr1 3000000 85347103 10 1000 . 3000000 85347103 117,112,179 46347
segway train --num-labels=2:4:1 test.genomedata traindir_nlabel
sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `x86_64-conda_cos6-linux-gnu-c++ -E -x assembler-with-cpp -DCARD_SEG=slice(2, 4, 1) -DCARD_SUBSEG=1 -DCARD_FRAMEINDEX=2000000 -DSEGTRANSITION_WEIGHT_SCALE=1.0 -Itraindir_nlabel -I. traindir_nlabel/segway.str'
Unexpected EOF Error: expecting GM magic keyword at line 1
Exiting Program
Dear Roberts and Michael,
Thanks for the pointer! Since we have multiple assay types (ChIP-seq, RNA-seq, etc), can we use SegRNA for ChIP-seq assays together with RNA-seq?
Best,Ran
From: Roberts, Eric <[log in to unmask]>
Sent: Tuesday, June 7, 2022 11:31 AM
To: Michael Hoffman <[log in to unmask]>
Cc: ranz0 <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
This is the relevant section in the docs about the --reverse-world option and concatenation.
Not sure why it didn't come up in the search!
Eric
From: Michael Hoffman <[log in to unmask]>
Sent: Tuesday, June 7, 2022 11:08 AM
To: Roberts, Eric <[log in to unmask]>
Cc: Ran Zhang <[log in to unmask]>
Subject: [External] Re: Rejected posting to [log in to unmask][Bcc Bill]
Eric can you please help with this? M
Thanks! I'm cc'ing Ran, postdoc in my lab, so she knows about this. Ran, here is the preprint: https://www.biorxiv.org/content/10.1101/2020.07.28.225193v2
Michael, I am not sure which documents you are referring to. I searched the readthedocs for Segway for "reverse-world" but came up empty:
https://segway.hoffmanlab.org/doc/3.0.4/search.html?q=reverse-world&check_keywords=yes&area=default#
Can you help?
Thanks.
Bill
Yeah unfortunately if we let anyone send to it the spam is out of control.
We have a preprint on SegRNA in fact! The - - reverse-world option is what you need, should be described in the docs.Michael
Hi Michael,
I tried to figure out how to send a support message about Segway, but it seems like I can't ask a question without subscribing to the list. Is that right? Seems like a lot of overhead!
Anyway, the question (below) is whether RNA-seq is supported. Did you ever end up implementing the two-strand stuff for RNA-seq analysis?
Thanks!Bill
---------- Forwarded message ---------
From: LISTSERV.UTORONTO.CA LISTSERV Server (16.0) <[log in to unmask]>
Date: Wed, Jun 1, 2022 at 8:39 PM
Subject: Rejected posting to [log in to unmask]
To: William Noble <[log in to unmask]>
You are not authorized to send mail to the SEGWAY-L list from your
[log in to unmask] account. You might be authorized to post to the list from another
account, or perhaps when using another mail program configured to use a
different email address. However, LISTSERV has no way to associate this other
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---------- Forwarded message ----------
From: William Stafford Noble <[log in to unmask]>
To: [log in to unmask]
Cc:
Bcc:
Date: Wed, 1 Jun 2022 20:39:03 -0700
Subject: RNA-seq segmentation
Does Segway support RNA-seq segmentation? I know there were plans to do so, but I don't know (remember?) whether those plans were ever completed. We have data from four tissues and five assay types, and we were thinking of applying Segway to it, but one of the assays is RNA-seq.
Thanks.Bill
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