Comments (5)
We should investigate why tge ucsc browser places these restrictions on sequence names. It might be unnecessary an loses important information
-----Original Message-----
From: Joel Armstrong [email protected]
To: benedictpaten/cactus [email protected]
Sent: Wed, 01 Oct 2014 9:53 AM
Subject: [cactus] People find the cactus header requirements + error messages confusing (#8)
Low priority, but: The requirements that cactus has for fasta headers are somewhat confusing to users, and it's especially bad since a lot of NCBI/genbank identifiers break the requirements. We should look into making the error messages more straightforward and provide a suggested solution (replacing .'s and/or spaces with underscores, probably).
We can't do much about the browser's requirements for the "." syntax, but we could look into using [nameparse=full]
instead of [nameparse=darkspace]
for lastz to attempt to get rid of the "first word of a header must be unique" rule. This would make parsing the cigars difficult, though, so it may be more trouble than it's worth.
Reply to this email directly or view it on GitHub:
#8
from cactus.
Brian said a while back they might cause problems because mySQL uses "." as a separator between db and table. Not sure if any of the assembly hub stuff actually goes through mySQL, but maybe it goes through code that is expecting a ".table" kind of syntax.
from cactus.
They quit making tables spit by chromosome years ago. We should be able to
drop this restriction. It's especially bad for assemblyHubs where there
are no mysql tables.
Joel Armstrong [email protected] writes:
Brian said a while back they might cause problems because mySQL uses "." as a
separator between db and table. Not sure if any of the assembly hub stuff
actually goes through mySQL, but maybe it goes through code that is expecting a
".table" kind of syntax.—
Reply to this email directly or view it on GitHub.*
from cactus.
OK, I've tested it a bit and it looks like there is no reason for that particular "ucscNames" restriction anymore. (Other than exported MAFs being hard to parse, but that isn't so bad.) Removing that will make things much better, there are so many headers with "."s in them that broke things before...
from cactus.
OK, we now ignore the "ucscNames" restriction by default, but enforce some requirements for characters that the UCSC browser still doesn't like, like "|". We should look into fixing the browser to allow "|" characters especially, since genbank sequences often have those in their identifiers.
The "first word must be unique" requirement is harder to get rid of, and it follows the FASTA spec, so I think it's more understandable.
from cactus.
Related Issues (20)
- filter_paf_deletions request insufficient memory HOT 4
- question about cactus-hal2maf HOT 4
- cactus-hal2chains taking a long time HOT 1
- How to keep large AMBIGUOUS contig in pangenome graph HOT 3
- The accelerator {'count': 1, 'kind': 'gpu', 'api': 'cuda', 'brand': 'nvidia'} could not be provided (Singularity container ) HOT 3
- Running the docker image in Singularity HOT 1
- Why it seems lastz works only use one core HOT 2
- RuntimeError: can't start new thread HOT 9
- Adjusting config.xml to allow multifurcations HOT 4
- Question about final gfa files from Minigraph-Cactus HOT 1
- system-specified memory limit or not? HOT 4
- vcf-bubwave does not raise error when it fails HOT 17
- Good practice for Reference-Mapped Short Read Genomes? HOT 2
- raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out)) HOT 2
- vcf location problem in Minigraph catus HOT 1
- ValueError in redMasking.py due to invalid literal for int() with base 10 HOT 2
- How to find halLiftover from cactus install? HOT 1
- maybe the "path" do not exist in the gfa ?
- Large variation in run time and data recovery of cactus-hal2maf when switching reference genomes HOT 1
- Cactus-pangenome fails at make_vcf step only on real data HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cactus.