Comments (10)
Hi
pfscanV3 (pfscan rewritten in C++ with heuristic improvements) should not have such issue.
Could you use that one or the old pfscan is mandatory for you?
from pftools3.
Hi,
Thanks for your suggestion. In fact, most of the time, we don't use use pfscan
directly but we use interproscan
which in turns use ps_scan.pl
which in turns use pfscan
(hence we also reported #9).
Is there a way to force interproscan
to use v3 ?
from pftools3.
Development of pftools V3 started years ago following a request of interproscan to speed up queries on Prosite.
So interproscan should have a way to switch to pftools v3 somewhere
from pftools3.
AFAICS, pftoolsV3
is not in the binaries provided by interproscan so I think that this is not possible right now. I have asked them.
from pftools3.
@duboism thanks for this update. We had tested pfsearchV3 in InterProScan probably at v3.0 when it was at ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/pftoolsV3, but we found it wasn't stable enough to include in InterProScan for public use. We had identified errors which were fixed and the fixed version sent to us but the files and the documentation at ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/pftoolsV3 were not updated.
We will now test the new version
from pftools3.
Hi @duboism
Patches have been applied to increase the filename size for pftools v2. The new size follows today usage on Linux.
Could you let us know if it works for you? This is in the master branch.
from pftools3.
Sorry, I missed the notification. I will be happy to help but I don't know how to use pfscan
. Can you provide a simple example ? I will then test with increasing file name length.
from pftools3.
Here are two examples coming from the test suite (files are in the tests/examples/ folder)
pfscan -s GTPA_HUMAN.dat prosite13.prf
pfscan -by -C 2 CVPBR322.embl ecp.prf
from pftools3.
I tested pfscan
with longer and longer filename. For the tag v3.2.5 (before #12), pfscan
starts to fail if the filename is longer than 512: one can clearly see that filename truncated to 512 in pfscan
and it returns 1. For the current master, the shell will start to fail when the filename is longer that 4096.
So I can confirm that it works now. 👍
from pftools3.
Great!
Thank you for testing
from pftools3.
Related Issues (17)
- pfscanV3 producing no matches for certain sequences HOT 3
- pfscanV3 message when run with a single profile HOT 2
- using ps_scan.pl to scan prosite patterns HOT 2
- Please include src/C/config.h.cmake inside release tarball HOT 3
- Build time test issues for version 3.2.6 HOT 9
- Calibrate DNA built profiles HOT 10
- Detecting the number of available cores HOT 17
- pfsearchV3 crashes on big databases HOT 4
- Error: Inconsistent alignment found HOT 4
- incomplete type compilation issue when compiled on Rocky Linux HOT 4
- Error compiling on OSX HOT 2
- -DUSE_AFFINITY=OFF -> error: field 'LastModification' has incomplete type HOT 9
- pfscanV3 error HOT 2
- pfscanV3 cannot use motif files that contain patterns HOT 1
- cpu detection failure HOT 2
- pfscan errors are not catched HOT 11
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 pftools3.