generating random sequences
by xu_jianzhen
Hi,galaxy users,
I'am wondering if there is a tool for generating random genome sequence or from a specific region(i.e. all promoter region).I known there is 'random intervals' in 'ENCODE Tools'.But the problem is it seems restricted to generating random sequence from 'ENCODE Regions' while i'd prefer whole genenome region.
By the way, what is the statistical model for generating this random sequence? can i just random generate a series of genome coordinates and then extract the correponding sequences?
If you had read some research articles descripting the random procedure, please suggest for me.
Regards,
Xu Jianzhen
GIBH,CAS
12 years, 9 months
extracting alignments from Multiz with RefSeq annotation
by Vesselin Baev
Dear all,
I'm wondering when I extract a alignments with coorfinates (for
refseqs) from Multiz from genome-wide alignments I can make fasta MAFs
with info-line with coordinates but never looking like this:
>NM_017821.0.1 hg17.chr1 206501580 206501621 - 245522847 mm5.chr4
122200029 122200071 + 154141344 rn3.chr5 143135020 143135060 +
173106704 canFam1.chr15 6850518 6850559 + 67237905
CCTGCCCCTATTGTAAGTCAATTAATA-AAAAGAGCCATCTGG
CTTGCCTCTATGATAAACCAGTTAATATAAAAGTGTCACATGG
CTTGCCTCTGTTATAAGCCACTTAATA--AAAGTGTCACATGG
CCTGCCTCTCATAGGAAGCAAGTAATG-AAAAGAGCCATCTGG
>NM_004070.0.0 hg17.chr1 16105460 16105489 + 245522847 mm5.chr4
14280459 14280491 - 154141344 rn3.chr5 12802003 12802032 - 173106704
canFam1.chr2 5413700 5413729 - 87725193
GCCGGCCCAGCAAGATGAAACAG---GGCACCC
GTCAGCCTGGGGGGGGTCGGCAGCCTGGCACCC
GTCAGCCTGG---GAGTCGGCAGCCTGGCGCCC
GCCAGCCCAGCAAGATGAAACAG---GGTGGCC
How to make this? I have failed trying do this...
Vesko
--
------------------------------------------------
Dr. Vesselin Baev
University of Plovdiv
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 43 80 945
Skype: vesselin_baev
vebaev(a)gmail.com
baev(a)uni-plovdiv.bg
12 years, 9 months
naming MAF blocks
by Vesselin Baev
Dear all,
I heve done this in steps:
1. Go to genome.ucsc.edu and select the tables link.
2. Select the clade, organism, and assembly that you are interested in.
3. Select Genes and Gene Predictions from the group.
4. Select UCSC genes from track.
5. From region select genome.
-from Paste List I put my needed list of genes.
6. From output format select custom track.
7. Select get output.
8. On that page put in utr3 in the name, and select 3' UTR exons.
9. Select get custom track in table browser.
10. Select Comparative Genomics from group.
11. Select Conservation from track
12. Select 28-multiz from table.
13. Click on the create button in the intersection line.
14. Select Custom Tracks from the group.
15. Select utr3 from the track.
for example I have 100 genes (in Paste List) that I get UTRs from them
and use in intersection line.
I got MAFs that exceed 100 pieces, every MAF have coordinates, but how
to see which MAF blocks are for the first UTR (of some gene)? is there
a way to name the MAF blocks?
Vesko
--
------------------------------------------------
Dr. Vesselin Baev
University of Plovdiv
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 43 80 945
Skype: vesselin_baev
vebaev(a)gmail.com
baev(a)uni-plovdiv.bg
12 years, 9 months
use with local browser mirror
by Keith Lamont
Hi all,
Is it possible to customize Galaxy to use a mirror of the genome
browser?
Thanks,
Keith Lamont
12 years, 9 months
SVN Access not working?
by Jacob Biesinger
Hi.
I've had Galaxy in my sights for some time now and I've finally found some
time to sit down with it. I'm a Senior in Bioinformatics at BYU and have
done a lot of the work that Galaxy is designed to do by hand in Python. I'm
very interested in developing more tools for Galaxy, but as I sat down to
check out the source, I'm getting the following error:
$ svn co http://www.bx.psu.edu/svn/universe/galaxy/trunk galaxy
svn: REPORT request failed on '/svn/universe/!svn/vcc/default'
svn: REPORT of '/svn/universe/!svn/vcc/default': Could not read status line:
connection was closed by server. (http://www.bx.psu.edu)
There is nothing wrong with my svn client. I'm able to check out and update
other projects as usual. I'd love to get started ASAP.
Thanks for your time and the excellent product!
-Jake Biesinger
12 years, 9 months
[Bug] Errors with Cheetah on Intel Mac?
by Jacob Biesinger
Hi.
I just checked out the latest version of galaxy and went through
installation. I'm writing to note the issues I've encountered thus far.
A number of eggs were missing for my platform (Intel Mac OS 10.4, python
2.5) and I had to scramble a number of eggs. These included the following:
pycrypto
lzo_python
Cheetah
pysqlite
bx_python
Scrambling my own eggs worked fine except for with pysqlite. I grabbed
version 3.5.4 of sqlite3.c file and built a static pysqlite egg file.
When I first ran run.sh, the web server loaded just fine. But on attempting
to upload a file, I got the following dump, which says to me that galaxy is
using a local install of Cheetah rather than the egg that I scrambled:
URL: http://localhost:8080/tool_runner?tool_id=upload1
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py',
line 364 in respond
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/debug/prints.py',
line 98 in __call__
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/wsgilib.py',
line 539 in intercept_output
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Beaker-0.5-py2.5.egg/beaker/session.py',
line 103 in __call__
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/recursive.py',
line 80 in __call__
File
'/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpexceptions.py',
line 632 in __call__
File '/Users/wjb/Projects/galaxy/lib/galaxy/web/framework/base.py', line 123
in __call__
body = method( trans, **kwargs )
File '/Users/wjb/Projects/galaxy/lib/galaxy/web/controllers/tool_runner.py',
line 42 in index
return trans.fill_template( template, history=history, toolbox=toolbox,
tool=tool, util=util, **vars )
File '/Users/wjb/Projects/galaxy/lib/galaxy/web/framework/__init__.py', line
356 in fill_template
searchList=[kwargs, self.template_context, dict(caller=self, t=self,
h=webhelpers, util=util, request=self.request, response=self.response,
app=self.app)] )
File
'/opt/local/lib/python2.5/site-packages/Cheetah-2.0.1-py2.5-macosx-10.3-i386.egg/Cheetah/Template.py',
line 1192 in __init__
self._compile(source, file, compilerSettings=compilerSettings)
File
'/opt/local/lib/python2.5/site-packages/Cheetah-2.0.1-py2.5-macosx-10.3-i386.egg/Cheetah/Template.py',
line 1480 in _compile
keepRefToGeneratedCode=True)
File
'/opt/local/lib/python2.5/site-packages/Cheetah-2.0.1-py2.5-macosx-10.3-i386.egg/Cheetah/Template.py',
line 777 in compile
raise e
IndentationError: expected an indented block
(_Users_wjb_Projects_galaxy_templates_tool_form_tmpl.py, line 226)
I removed my /opt/local installation of Cheetah (and a few other
dependencies in /opt/local that I thought might affect building). I then
started again on installation by removing the eggs directory and running
setup.sh again. The above listed dependencies were not found again. I
scrambled them (including pysqlite as static) and tried to run run.sh once
again. Now I am getting the following error:
Using eggs in py2.5-noplatform
Using eggs in py2.5-macosx-10.3-i386-ucs2
Checking Galaxy eggs
All eggs are up to date for this revision of Galaxy
python path:
/Users/wjb/Projects/galaxy/lib:/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform:/Users/wjb/Projects/galaxy/eggs/py2.5-macosx-10.3-i386-ucs2
path:
/opt/local/bin:/opt/local/sbin:/usr/local/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/texbin:/Library/Frameworks/Python.framework/Versions/Current/bin:/usr/local/mysql/bin:/opt/local/lib/postgresql82/bin:/depot/apps/i386/bin:/home/universe/darwin-i386/EMBOSS-5.0.0/bin:/home/universe/darwin-i386/ImageMagick/bin:/home/universe/darwin-i386/PAML/paml3.15/bin
Traceback (most recent call last):
File "./scripts/paster.py", line 11, in <module>
command.run()
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py",
line 78, in run
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py",
line 117, in invoke
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py",
line 212, in run
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py",
line 227, in command
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py",
line 250, in loadapp
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py",
line 193, in loadapp
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py",
line 213, in loadobj
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py",
line 237, in loadcontext
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py",
line 267, in _loadconfig
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py",
line 397, in get_context
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py",
line 439, in _context_from_explicit
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py",
line 18, in import_string
File "/Users/wjb/Projects/galaxy/lib/pkg_resources.py", line 1912, in load
try:
File "/Users/wjb/Projects/galaxy/lib/galaxy/web/__init__.py", line 5, in
<module>
from framework import expose, json, url_for, error, FormBuilder
File "/Users/wjb/Projects/galaxy/lib/galaxy/web/framework/__init__.py",
line 9, in <module>
from Cheetah.Template import Template
File "build/bdist.macosx-10.3-i386/egg/Cheetah/Template.py", line 47, in
<module>
File "build/bdist.macosx-10.3-i386/egg/Cheetah/ErrorCatchers.py", line 16,
in <module>
File
"/Users/wjb/Projects/galaxy/eggs/py2.5-macosx-10.3-i386-ucs2/Cheetah-1.0-py2.5-macosx-10.3-i386.egg/Cheetah/NameMapper.py",
line 146
SyntaxError: from __future__ imports must occur at the beginning of the file
I am still a bit concerned by my path and python_path variables, but it
doesn't look like this error is related to them. Any ideas? I'm afraid I've
spent too much time on this alrady and if I can't find a decent solution, I
will have to bag this pathwayfor a few more months.
Thanks for your time!
-Jake Biesinger
12 years, 9 months
Moderated posts?
by Jacob Biesinger
I signed up for an account with this email address, but the two messages
I've sent to the list are awaiting moderator authorization. Is that normal?
12 years, 9 months
