obitools4/doc/book/comm_sampling.qmd

# Sequence sampling and filtering 

## `obigrep` -- filters sequence files according to numerous conditions

{{< include ../lib/descriptions/_obigrep.qmd >}}

### The options usable with `obigrep`

#### Selecting sequences based on their caracteristics

Sequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.

**Selection based on the sequence**


Sequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (*e.g* `AACCTT`). But the usage of regular patterns allows for looking for more complex pattern. As example, `A[TG]C+G` matches a `A`, followed by a `T` or a `G`, then one or several `C` and endly a `G`.

{{< include ../lib/options/selection/_sequence.qmd >}}

*Examples:*

: Selects only the sequence records that contain an *EcoRI* restriction site.

```bash   
obigrep -s 'GAATTC' seq1.fasta > seq2.fasta
```
    
: Selects only the sequence records that contain a stretch of at least 10 ``A``.    
    
```bash   
obigrep -s 'A{10,}' seq1.fasta > seq2.fasta
```

: Selects only the sequence records that do not contain ambiguous nucleotides.
    
```bash   
obigrep -s '^[ACGT]+$' seq1.fasta > seq2.fasta
```


{{< include ../lib/options/selection/_min-count.qmd >}}

{{< include ../lib/options/selection/_max-count.qmd >}}

*Examples*

: Selecting sequence records representing at least five reads in the dataset.

```bash
obigrep -c 5 data_SPER01.fasta > data_norare_SPER01.fasta
```