${PHILOSOPHER} database --id UP000001940 does not download full reference proteome anymore

[cpanse]

${PHILOSOPHER} database --id UP000001940 does not download full reference proteome anymore
input:

#!/bin/bash

set -euxo pipefail

PHILOSOPHER=/usr/local/nesvilab/philosopher_v4.3.0/philosopher-v4.3.0-RC

${PHILOSOPHER} workspace --clean
${PHILOSOPHER} workspace --init --temp $PWD
${PHILOSOPHER} database --id UP000001940
grep "^>" U*.fas|cut -c -3|uniq -c

output:

cpanse@fgcz-c-073:/scratch/cpanse/philosopher/UP000001940 > bash runme.bash 
+ PHILOSOPHER=/usr/local/nesvilab/philosopher_v4.3.0/philosopher-v4.3.0-RC
+ /usr/local/nesvilab/philosopher_v4.3.0/philosopher-v4.3.0-RC workspace --clean
INFO[15:56:30] Executing Workspace  v4.3.0                  
WARN[15:56:30] There is a new version of Philosopher available for download: https://philosopher/releases 
INFO[15:56:30] Removing workspace                           
INFO[15:56:30] Done                                         
+ /usr/local/nesvilab/philosopher_v4.3.0/philosopher-v4.3.0-RC workspace --init --temp /scratch/cpanse/philosopher/UP000001940
INFO[15:56:31] Executing Workspace  v4.3.0                  
WARN[15:56:31] There is a new version of Philosopher available for download: https://philosopher/releases 
INFO[15:56:31] Creating workspace                           
INFO[15:56:31] Done                                         
+ /usr/local/nesvilab/philosopher_v4.3.0/philosopher-v4.3.0-RC database --id UP000001940
INFO[15:56:31] Executing Database  v4.3.0                   
WARN[15:56:31] contaminants are not going to be added to database 
INFO[15:56:31] Fetching database UP000001940                
INFO[15:56:36] Generating the target-decoy database         
INFO[15:56:36] Creating file                                
INFO[15:56:36] Processing decoys                            
INFO[15:56:37] Creating file                                
INFO[15:56:37] Done                                         
+ grep '^>' UP000001940.fas
+ cut -c -3
+ uniq -c
  22221 >tr

To Reproduce

see above

Expected behavior

output:

22221 >tr
4380 >sp

Please complete the following information:

cpanse@fgcz-c-073:/scratch/cpanse/philosopher/UP000001940 > /usr/local/nesvilab/philosopher_v4.3.0/philosopher-v4.3.0-RC version
INFO[15:59:45] Current Philosopher build and version         build=202207041335 version=v4.3.0
WARN[15:59:45] There is a new version of Philosopher available for download: https://philosopher/releases 

cpanse@fgcz-c-073:/scratch/cpanse/philosopher/UP000001940 > uname -a
Linux fgcz-c-073 5.4.121-0504121-generic #202105220633 SMP Sat May 22 10:38:55 UTC 2021 x86_64 GNU/Linux

Additional context

Don't you use unit tests?

[prvst]

@cpanse Nice catch, I see what's happening. The problem is a change in the behavior regarding the reviewed parameter. With the previous API, when reviewed was false, both Swisprot + Tremble were fetched at the same time. With the new API, reviewed = false fetches only the Tremble, go figures... I already patched the problem. A new release will be available tonight or tomorrow.

Thanks Christian.

Fixed. Added to v4.5.1

[cpanse]

@prvst, the credit goes to @tobiasko. Thank you! C

[tobiasko]

@prvst Could you estimate when v 4.5.1 will be released?

[prvst]

Not yet, but you can grab release candidates here. Every time an issue gets closed with a paragraph stating that it was fixed, then you'll find an RC in the URL