---
name: "obiaddtaxids"
section: "1"
platform: "linux"
package: "obitools"
version: "1.2.12+dfsg-2"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/obiaddtaxids"
---

# obiaddtaxids(1)

description of obiaddtaxids The obiaddtaxids command annotates sequence records with a taxid based on a taxon scientific name stored in the sequence record header. Taxonomic information linking a taxid to a taxon scientific name is stored in a database formatted as an ecoPCR database (see obitaxonomy) or a NCBI taxdump (see NCBI ftp site). The way to extract the taxon scientific name from the sequence record header can be specified by two options: For each sequence record, obiaddtaxids tries to match the extracted taxon scientific name with those stored in the taxonomic database. Otherwise,

## NAME

obiaddtaxids - description of obiaddtaxids

The *obiaddtaxids* command annotates sequence records with a *taxid* based on  a taxon scientific name stored in the sequence record header.

Taxonomic information linking a *taxid* to a taxon scientific name is stored in a  database formatted as an ecoPCR database (see obitaxonomy) or  a NCBI taxdump (see NCBI ftp site).

The way to extract the taxon scientific name from the sequence record header can be specified by two options:

- •

  By default, the sequence identifier is used. Underscore characters (**\_**) are substituted by spaces before looking for the taxon scientific name into the taxonomic database.

- •

  If the input file is an **OBITools** extended fasta format, the **-k** option specifies the attribute containing the taxon scientific name.

- •

  If the input file is a fasta file imported from the UNITE or from the SILVA web sites, the **-f** option allows specifying this source and parsing correctly the associated  taxonomic information.

For each sequence record, *obiaddtaxids* tries to match the extracted taxon scientific name  with those stored in the taxonomic database.

- •

  If a match is found, the sequence record is annotated with the corresponding *taxid*.

Otherwise,

- •

  If the **-g** option is set and the taxon name is composed of two words and only the  first one is found in the taxonomic database at the ‘genus’ rank, *obiaddtaxids*  considers that it found the genus associated with this sequence record and it stores this  sequence record in the file specified by the **-g** option.

- •

  If the **-u** option is set and no taxonomic information is retrieved from the  scientific taxon name, the sequence record is stored in the file specified by the  **-u** option.

*Example*

```
> obiaddtaxids -k species_name -g genus_identified.fasta \
               -u unidentified.fasta -d my_ecopcr_database \
               my_sequences.fasta > identified.fasta
```

Tries to match the value associated with the **species\_name** key of each sequence record  from the **my\_sequences.fasta** file with a taxon name from the ecoPCR database **my\_ecopcr\_database**.

- •

  If there is an exact match, the sequence record is stored in the **identified.fasta** file.

- •

  If not and the **species\_name** value is composed of two words, *obiaddtaxids*  considers the first word as a genus name and tries to find it into the taxonomic database.

  - •

    If a genus is found, the sequence record is stored in the **genus\_identified.fasta** file.

  - •

    Otherwise the sequence record is stored in the **unidentified.fasta** file.

## OBIADDTAXIDS SPECIFIC OPTIONS

- **-f \<FORMAT\>, --format=\<FORMAT\>**

  Format of the sequence file. Possible formats are:

  - •

    **raw**: for regular **OBITools** extended fasta files (default value).

  - •

    **UNITE**: for fasta files downloaded from the *UNITE web site*.

  - •

    **SILVA**: for fasta files downloaded from the *SILVA web site*.

- **-k \<KEY\>, --key-name=\<KEY\>**

  Key of the attribute containing the taxon name in sequence files in the **OBITools** extended fasta format.

- **-a \<ANCESTOR\>, --restricting\_ancestor=\<ANCESTOR\>**

  Enables to restrict the search of *taxids* under a specified ancestor.

  **\<ANCESTOR\>** can be a *taxid* (integer) or a key (string).

  - •

    If it is a *taxid*, this *taxid* is used to restrict the search for all the sequence records.

  - •

    If it is a key, *obiaddtaxids* looks for the ancestor *taxid* in the corresponding attribute. This allows having a different ancestor restriction for each sequence record.

- **-g \<FILENAME\>, --genus\_found=\<FILENAME\>**

  File used to store sequences with a match found for the genus.

  **CAUTION:**

  this option is not valid with the UNITE format.

- **-u \<FILENAME\>, --unidentified=\<FILENAME\>**

  File used to store sequences with no taxonomic match found.

## TAXONOMY RELATED OPTIONS

- **-d \<FILENAME\>, --database=\<FILENAME\>**

  ecoPCR taxonomy Database name

- **-t \<FILENAME\>, --taxonomy-dump=\<FILENAME\>**

  NCBI Taxonomy dump repository name

## COMMON OPTIONS

- **-h, --help**

  Shows this help message and exits.

- **--DEBUG**

  Sets logging in debug mode.

## OBIADDTAXIDS ADDED SEQUENCE ATTRIBUTE

- •

  taxid

## AUTHOR

The OBITools Development Team - LECA

## COPYRIGHT

2019 - 2015, OBITool Development Team