Bug#963028: marked as done (ITP: pychopper -- identify, orient and trim full-length Nanopore cDNA reads)
Your message dated Mon, 22 Jun 2020 21:00:10 +0000
with message-id <E1jnTY2-0006fW-Rb@fasolo.debian.org>
and subject line Bug#963028: fixed in pychopper 2.4.0-1
has caused the Debian Bug report #963028,
regarding ITP: pychopper -- identify, orient and trim full-length Nanopore cDNA reads
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
963028: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=963028
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Subject: ITP: pychopper -- identify, orient and trim full-length Nanopore cDNA reads
Package: wnpp
Owner: Steffen Moeller <moeller@debian.org>
Severity: wishlist
* Package name : pychopper
Version : 2.4.0
Upstream Author : Oxford Nanopore Technologies Ltd.
* URL : https://github.com/nanoporetech/pychopper
* License : MPL-2.0
Programming Lang: Python
Description : identify, orient and trim full-length Nanopore cDNA reads
Pychopper v2 is a tool to identify, orient and trim full-length Nanopore
cDNA reads. The tool is also able to rescue fused reads. The general
approach of Pychopper v2 is the following:
.
* Pychopper first identifies alignment hits of the primers across the
length of the sequence. The default method for doing this is using
nhmmscan with the pre-trained strand specific profile HMMs, included
with the package. Alternatively, one can use the edlib backend,
which uses a combination of global and local alignment to identify
the primers within the read.
* After identifying the primer hits by either of the backends, the
reads are divided into segments defined by two consecutive primer
hits. The score of a segment is its length if the configuration of
the flanking primer hits is valid (such as SPP,-VNP for forward reads)
or zero otherwise.
* The segments are assigned to rescued reads using a dynamic programming
algorithm maximizing the sum of used segment scores (hence the amount
of rescued bases). A crucial observation about the algorithm is that
if a segment is included as a rescued read, then the next segment
must be excluded as one of the primer hits defining it was "used
up" by the previous segment. This put constraints on the dynamic
programming graph. The arrows in read define the optimal path for
rescuing two fused reads with the a total score of l1 + l3.
.
A crucial parameter of Pychopper v2 is -q, which determines the
stringency of primer alignment (E-value in the case of the pHMM
backend). This can be explicitly specified by the user, however by
default it is optimized on a random sample of input reads to produce
the maximum number of classified reads.
Remark: This package is maintained by Debian Med Packaging Team at
https://salsa.debian.org/med-team/pychopper
--- End Message ---
--- Begin Message ---
Source: pychopper
Source-Version: 2.4.0-1
Done: Steffen Moeller <moeller@debian.org>
We believe that the bug you reported is fixed in the latest version of
pychopper, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 963028@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Steffen Moeller <moeller@debian.org> (supplier of updated pychopper package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 17 Jun 2020 23:41:37 +0200
Source: pychopper
Binary: python3-pychopper
Architecture: source all
Version: 2.4.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
python3-pychopper - identify, orient and trim full-length Nanopore cDNA reads
Closes: 963028
Changes:
pychopper (2.4.0-1) unstable; urgency=medium
.
* Initial release (Closes: #963028)
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--- End Message ---
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