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

# obicomplement(1)

description of obicomplement obicomplement reverse-complements the sequence records. By using the selection option set, it is possible to reverse complement only a subset of the sequence records included in the input file. The selected sequence are reversed complemented, others are stored without modification

## NAME

obicomplement - description of obicomplement

*obicomplement* reverse-complements the sequence records.

**TIP:**

The identifiers of the sequence records are modified by appending to them the **\_CMP** suffix.

**TIP:**

a attribute with key **complemented** and value sets to **True** is added on each reversed complemented sequence record.

By using the selection option set, it is possible to reverse complement only a subset of the sequence records included in the input file. The selected sequence are reversed complemented, others are stored without modification

*Example 1:*

```
> obicomplement seq.fasta > seqRC.fasta
```

Reverses complements all sequence records from the **seq.fasta** file and stores the  result to the **seqRC.fasta** file.

*Example 2:*

```
> obicomplement -s 'A{10,}$' seq.fasta > seqRC.fasta
```

Reverses complements sequence records from the **seq.fasta** file only if they finish by at least 10 **A**. Others sequences are stored without modification.

## 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.

## AUTHOR

The OBITools Development Team - LECA

## COPYRIGHT

2019 - 2015, OBITool Development Team