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Download and prepare PFAM-A database #71

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Robaina opened this issue Feb 22, 2023 · 1 comment
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Download and prepare PFAM-A database #71

Robaina opened this issue Feb 22, 2023 · 1 comment
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enhancement New feature or request good first issue Good for newcomers

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@Robaina
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Robaina commented Feb 22, 2023

Is your feature request related to a problem? Please describe.
Add support to download the PFAM-A database, besides the PGAP database, to be able to use PFAM models alongside TIGRFAM.

Describe the solution you'd like
Add support to download PFAM database, also automatically split original multi-HMM file into separate files (as required by pynteny search). This can be achieved in bash like this:

#!/bin/bash
# Input hmm file path as a param to this script

csplit --digits=2  --quiet --prefix=hmm $1 "////+1" "{*}"

while read -r id filename
do
    mv "$filename" "$id".hmm
done < <(awk '$1 == "ACC" {print $2,FILENAME; nextfile}' hmm*)

But ideally would be integrated in a dedicated python function.

@Robaina Robaina added enhancement New feature or request good first issue Good for newcomers labels Feb 22, 2023
@Robaina Robaina self-assigned this May 23, 2023
@Robaina
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Robaina commented Nov 3, 2023

Merged PR #93

@Robaina Robaina closed this as completed Nov 3, 2023
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Labels
enhancement New feature or request good first issue Good for newcomers
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