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PR2 exact species assignment now without taxa ending with sp. #599

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Jun 26, 2023
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PR2 exact species assignment now without taxa ending with sp. #599

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PR2 exact species assignment now without taxa ending with sp.
d4straub Jun 23, 2023
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Implement review suggestion
d4straub Jun 26, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#563](https://github.com/nf-core/ampliseq/pull/563) - Renamed DADA2 taxonomic classification files to include the chosen reference taxonomy abbreviation.
- [#567](https://github.com/nf-core/ampliseq/pull/567) - Renamed `--dada_tax_agglom_min` and `--qiime_tax_agglom_min` to `--tax_agglom_min` and `--dada_tax_agglom_max` and `--qiime_tax_agglom_max` to `--tax_agglom_max`
- [#598](https://github.com/nf-core/ampliseq/pull/598) - Updated Workflow figure with SINTAX and phylogenetic placement
- [#599](https://github.com/nf-core/ampliseq/pull/599) - For exact species assignment (DADA2's addSpecies) PR2 taxonomy database (e.g. `--dada_ref_taxonomy pr2`) now excludes any taxa that end with " sp.".

### `Fixed`

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3 changes: 2 additions & 1 deletion bin/taxref_reformat_pr2.sh
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I suggest to add a comment on the last part too, i.e. the awk part that removes " sp".

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Thanks, yes, will do!

Original file line number Diff line number Diff line change
Expand Up @@ -7,4 +7,5 @@ gunzip -c *dada2.fasta.gz > assignTaxonomy.fna

# For addSpecies(), the UTAX file is downloaded and reformated to only contain the id and species.
# The second two sed calls are to replace "_" with space only in the species name and not the last part of the id (overdoing it a bit, as I don't the id actually matters as long as it's unique).
gunzip -c *UTAX.fasta.gz | sed '/^>/s/>\([^;]*\);.*,s:\(.*\)/>\1 \2/' | sed 's/_/ /g' | sed 's/ \([A-Z]\) /_\1 /' > addSpecies.fna
# The awk part removes any entries (sequence name and sequence) that have a sequence name ending with " sp."
gunzip -c *UTAX.fasta.gz | sed '/^>/s/>\([^;]*\);.*,s:\(.*\)/>\1 \2/' | sed 's/_/ /g' | sed 's/ \([A-Z]\) /_\1 /' | awk '!/ sp.\n/' RS=">" ORS=">" > addSpecies.fna
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