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

# obiconvert(1)

description of obiconvert obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats. Input files can be in : obiconvert converts those files to the : If no file name is specified, data is read from standard input. Examples:

## NAME

obiconvert - description of obiconvert

*obiconvert* converts sequence files to different output formats. See the documentation for more details on the different formats.

Input files can be in :

- •

  *fasta* format

- •

  *extended OBITools fasta* format

- •

  Sanger *fastq* format

- •

  Solexa *fastq* format

- •

  *ecoPCR* format

- •

  *ecoPCR* database format

- •

  *GenBank* format

- •

  *EMBL* format

*obiconvert* converts those files to the :

- •

  *extended OBITools fasta* format

- •

  Sanger *fastq* format

- •

  *ecoPCR* database format

If no file name is specified, data is read from standard input.

*Examples:*

```
> obiconvert --ecopcrdb --fasta-output \
  'my_ecopcr_database' > sequences.fasta
```

Converts an ecoPCR database in a sequence file in *extended OBITools fasta* format.

## TAXONOMY RELATED OPTIONS

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

  ecoPCR taxonomy Database name

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

  NCBI Taxonomy dump repository name

## OPTIONS TO SPECIFY INPUT FORMAT

### Restrict the analysis to a sub-part of the input file

- **--skip \<N\>**

  The N first sequence records of the file are discarded from the analysis and not reported to the output file

- **--only \<N\>**

  Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the *–skip* option.

### Sequence annotated format

- **--genbank**

  Input file is in genbank format.

- **--embl**

  Input file is in embl format.

### fasta related format

- **--fasta**

  Input file is in fasta format (including OBITools fasta extensions).

### fastq related format

- **--sanger**

  Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers).

- **--solexa**

  Input file is in fastq format produced by Solexa (Ga IIx) sequencers.

### ecoPCR related format

- **--ecopcr**

  Input file is in ecoPCR format.

- **--ecopcrdb**

  Input is an ecoPCR database.

### Specifying the sequence type

- **--nuc**

  Input file contains nucleic sequences.

- **--prot**

  Input file contains protein sequences.

## OPTIONS TO SPECIFY OUTPUT FORMAT

### Standard output format

- **--fasta-output**

  Output sequences in **OBITools** fasta format

- **--fastq-output**

  Output sequences in Sanger fastq format

### Generating an ecoPCR database

- **--ecopcrdb-output=\<PREFIX\_FILENAME\>**

  Creates an ecoPCR database from sequence records results

### Miscellaneous option

- **--uppercase**

  Print sequences in upper case (default is lower case)

## COMMON OPTIONS

- **-h, --help**

  Shows this help message and exits.

- **--DEBUG**

  Sets logging in debug mode.

## AUTHOR

The OBITools Development Team - LECA

## COPYRIGHT

2019 - 2015, OBITool Development Team