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Complete release notes and change obiannotate options accordingly

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Former-commit-id: 947db1f4606d57893cf758df57a4c954e3949e6b
This commit is contained in:
Eric Coissac
2023-05-02 11:01:26 +02:00
parent 60c187404d
commit bffcab1096
2 changed files with 15 additions and 1 deletions
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14
Release-notes.md
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@ -31,6 +31,20 @@
obidistribute --pattern "pcr_reads/sample_%s_R1.fastq" -c sample tagged_library_R1.fastq obidistribute --pattern "pcr_reads/sample_%s_R1.fastq" -c sample tagged_library_R1.fastq
obidistribute --pattern "pcr_reads/sample_%s_R2.fastq" -c sample tagged_library_R2.fastq obidistribute --pattern "pcr_reads/sample_%s_R2.fastq" -c sample tagged_library_R2.fastq
``` ```
- Adding of two options **--add-lca-in** and **--lca-error** to `obiannotate`. These options aim to help during
construction of reference database using `obipcr`. On obipcr output, it is commonly run obiuniq. To merge
identical sequences annotated with different taxids, it is now possible to use the following strategie :
```{bash}
obiuniq -m taxid myrefdb.obipcr.fasta \
| obiannotate -t taxdump --lca-error 0.05 --add-lca-in taxid \
> myrefdb.obipcr.unique.fasta
```
The `obiuniq` call merge identical sequences keeping track of the diversity of the taxonomic annotations in the
`merged_taxid` slot, while `obiannotate` loads a NCBI taxdump and computes the lowest common ancestor of the taxids represented in `merged_taxid`. By specifying **--lca-error** 0.05, we indicate that we allow for at most 5% of the taxids disagreeing with the computed LCA. The computed LCA is stored in the slot specified as a parameter of the option **--add-lca-in**. Scientific name and actual error rate corresponding to the estimated LCA are also stored in the sequence annotation.
### Enhancement ### Enhancement
- Rename the `forward_mismatches` and `reverse_mismatches` from instanced by `obimutiplex` into - Rename the `forward_mismatches` and `reverse_mismatches` from instanced by `obimutiplex` into

2
pkg/obitools/obiannotate/options.go
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@ -41,7 +41,7 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
options.StringVar(&_ahoCorazick, "aho-corasick", _ahoCorazick, options.StringVar(&_ahoCorazick, "aho-corasick", _ahoCorazick,
options.Description("Adds an aho-corasick attribut with the count of matches of the provided patterns.")) options.Description("Adds an aho-corasick attribut with the count of matches of the provided patterns."))
options.StringVar(&_lcaSlot, "add-lca", _lcaSlot, options.StringVar(&_lcaSlot, "add-lca-in", _lcaSlot,
options.ArgName("SLOT_NAME"), options.ArgName("SLOT_NAME"),
options.Description("From the taxonomic annotation of the sequence (taxid slot or merged_taxid slot), "+ options.Description("From the taxonomic annotation of the sequence (taxid slot or merged_taxid slot), "+
"a new slot named <SLOT_NAME> is added with the taxid of the lowest common ancester corresponding "+ "a new slot named <SLOT_NAME> is added with the taxid of the lowest common ancester corresponding "+