bb_get_fasta_seq - ampinzonv/BB3 GitHub Wiki
Function: bb_get_fasta_seq
Extract sequence lines from a FASTA file, excluding headers.
๐ Description
This function returns only the raw sequence lines from a FASTA file, omitting any lines that start with >.
๐ฅ Input
- A FASTA file (e.g. sequences, contigs, reads).
- Use
--input -for STDIN.
๐ค Output
- Only sequence lines, no headers.
๐งช Examples
bb_get_fasta_seq --input sequences.fasta
cat sequences.fasta | bb_get_fasta_seq --input -
bb_get_fasta_seq --input sequences.fasta --outfile seqs_only.txt
โ๏ธ Usage
bb_get_fasta_seq --input FILE [--outfile FILE] [--quiet] [--force]
๐งต Options
| Option | Description |
|---|---|
--input FILE |
Input FASTA file or - for STDIN (required) |
--outfile FILE |
Output file path (optional, default: STDOUT) |
--quiet |
Suppress log messages |
--force |
Overwrite existing output file |
๐ Notes
- This function is useful when the sequence alone is needed, e.g., for further alignment or counting tasks.