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

# obicount(1)

description of obicount obicount counts the number of sequence records and/or the sum of the count attributes. Example:

## NAME

obicount - description of obicount

*obicount* counts the number of sequence records and/or the sum of the **count** attributes.

*Example:*

```
> obicount seq.fasta
```

Prints the number of sequence records contained in the **seq.fasta**  file and the sum of their **count** attributes.

## OBICOUNT SPECIFIC OPTIONS

- **-a, --all**

  Prints only the sum of **count** attributes. If a sequence has no *count* attribute, its default count is 1.

  *Example:*

  ```
  > obicount -a seq.fasta
  ```

  For all sequence records contained in the **seq.fasta** file, prints only the sum of **count** attributes.

- **-s, --sequence**

  Prints only the number of sequence records.

  *Example:*

  ```
  > obicount -s seq.fasta
  ```

  Prints only the number of sequence records contained in the **seq.fasta** file.

## 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.

## COMMON OPTIONS

- **-h, --help**

  Shows this help message and exits.

- **--DEBUG**

  Sets logging in debug mode.

## OBICOUNT ADDED SEQUENCE ATTRIBUTE

- •

  count

## AUTHOR

The OBITools Development Team - LECA

## COPYRIGHT

2019 - 2015, OBITool Development Team