Usage:¶

pullseq -i <input fasta/fastq file> -n <header names to select>

pullseq -i <input fasta/fastq file> -m <minimum sequence length>

pullseq -i <input fasta/fastq file> -g <regex name to match>

pullseq -i <input fasta/fastq file> -m <minimum sequence length> -a <max sequence length>

pullseq -i <input fasta/fastq file> -t

cat <names to select from STDIN> | pullseq -i <input fasta/fastq file> -N

Options:

-i, --input,

Input fasta/fastq file (required)

-n, --names,

File of header id names to search for

-N, --names_stdin, Use STDIN for header id names

-g, --regex,

Regular expression to match (PERL compatible; always case-insensitive)

-m, --min,

Minimum sequence length

-a, --max,

Maximum sequence length

-l, --length,

Sequence characters per line (default 50)

-c, --convert,

Convert input to fastq/fasta (e.g. if input is fastq, output will be fasta)

-q, --quality,

ASCII code to use for fasta->fastq quality conversions

-e, --excluded,

Exclude the header id names in the list (-n)

-t, --count,

Just count the possible output, but don't write it

-h, --help,

Display this help and exit

-v, --verbose,

Print extra details during the run

--version,

Output version information and exit