Public bug reported:
On ubuntu 20.04.2, ncbi-blast+ 2.9.0-2
It appears that the parsing logic in the script was broken by the ncbi
entrez api at some point. When running this script with -n [species], it
returns the number of results and no more. Running the script included
with the latest version, 2.12.0, functions correctly with its modified
parsing.
Best way to resolve this is likely to just put the 2.12.0 script in the
package. Attached.
ProblemType: Bug
DistroRelease: Ubuntu 20.04
Package: ncbi-blast+ 2.9.0-2
ProcVersionSignature: Ubuntu 5.8.0-1036.38~20.04.1-azure 5.8.18
Uname: Linux 5.8.0-1036-azure x86_64
ApportVersion: 2.20.11-0ubuntu27.18
Architecture: amd64
CasperMD5CheckResult: pass
Date: Thu Jul 1 20:15:40 2021
InstallationDate: Installed on 2021-06-29 (1 days ago)
InstallationMedia: Ubuntu-Server 20.04.2 LTS "Focal Fossa" - Release amd64
(20210201.2)
ProcEnviron:
SHELL=/bin/bash
LANG=en_US.UTF-8
TERM=xterm-256color
XDG_RUNTIME_DIR=
PATH=(custom, no user)
SourcePackage: ncbi-blast+
UpgradeStatus: No upgrade log present (probably fresh install)
** Affects: ncbi-blast+ (Ubuntu)
Importance: Undecided
Status: New
** Tags: amd64 apport-bug focal patch uec-images
** Patch added: "script from 2.12.0"
https://bugs.launchpad.net/bugs/1934402/+attachment/5508502/+files/get_species_taxids.sh
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https://bugs.launchpad.net/bugs/1934402
Title:
get_species_taxids does not print all information when invoked with -n
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