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Fix gtdb bacteria info only #711

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merged 3 commits into from
Mar 18, 2024
Merged

Fix gtdb bacteria info only #711

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85791f9
updated code for collecting data from gtdb
Mar 18, 2024
48d02b8
updated comment
Mar 18, 2024
0f4346c
updated CHANGELOG
Mar 18, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Changed`

- [#677](https://github.com/nf-core/ampliseq/pull/677) - Added cut_its information to SDBI export
- [#711](https://github.com/nf-core/ampliseq/pull/711) - Changed code in taxref_reformat_gtdb.sh so it can take both bacteria and Archaea. Check issue [#708](https://github.com/nf-core/ampliseq/issues/708) for more info.

### `Fixed`

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6 changes: 3 additions & 3 deletions bin/taxref_reformat_gtdb.sh
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@@ -1,6 +1,6 @@
#!/bin/sh

# Reads the ar122 and bac120 SSU fasta files from GTDB (after first untarring)
# Reads the ar* and bac* SSU fasta files from GTDB (after first untarring)
# and outputs two new fasta files, one suitable for DADA2's assignTaxonomy()
# and addSpecies() functions.

Expand All @@ -10,7 +10,7 @@ for f in *.tar.gz; do
done

# Write the assignTaxonomy() fasta file: assignTaxonomy.fna
cat ar122*.fna bac120*.fna | sed '/^>/s/>[^ ]\+ \([^[]\+\) \[.*/>\1/' | sed '/^>/s/ \[.*//' | sed 's/[a-z]__//g' > assignTaxonomy.fna
cat ar*.fna bac*.fna | sed '/^>/s/>[^ ]\+ \([^[]\+\) \[.*/>\1/' | sed '/^>/s/ \[.*//' | sed 's/[a-z]__//g' > assignTaxonomy.fna

# Write the addSpecies() fasta file: addSpecies.fna
cat ar122*.fna bac120*.fna | sed '/^>/s/>\([^ ]\+\) .*;s__\([^[]\+\) \[.*/>\1 \2/' > addSpecies.fna
cat ar*.fna bac*.fna | sed '/^>/s/>\([^ ]\+\) .*;s__\([^[]\+\) \[.*/>\1 \2/' > addSpecies.fna
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