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Refactoring codes for removing buffer size options. An some other changes...

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Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
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Eric Coissac
2023-03-07 11:12:13 +07:00
parent 9811e440b8
commit d88de15cdc
52 changed files with 1172 additions and 421 deletions
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doc/book/comm_sampling.qmd
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@ -10,13 +10,39 @@
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 >}}
Example
*Examples*
: Selecting sequence records representing at least five reads in the dataset.