trim

Trim sequences on the left and/or right (single range) or extract and concatenate several ranges

Usage: st trim [OPTIONS] <RANGES> [INPUT]...

Options:
  -h, --help  Print help

'Trim' command options:
  -e, --exclusive   Exclusive trim range: excludes start and end positions from
                    the output sequence. In the case of unbounded ranges
                    (`start:` or `:end`), the range still extends to the
                    complete end or the start of the sequence
  -0, --zero-based  Interpret range as 0-based, with the end not included
  <RANGES>      Range(s) in the form 'start:end' or 'start:' or ':end', Multiple
                ranges can be supplied as comma-delimited list:
                'start:end,start2:end2', etc. The start/end positions can be
                defined by variables/functions (start_var:end_var), or
                variables/functions may return the whole range (e.g. stored as
                header attribute 'attr(range)'), or even a list of ranges (e.g.
                'attr(range_list)'). *Note* that with the FASTA format, multiple
                trim ranges must be in order (from left to right) and cannot
                overlap

See this page for the options common to all commands.

The trim ranges always include the start and end coordinates unless -0 is specified. Coordinates can be negative to indicate an offset from the end. See explanation of ranges for more details.

Example: primer trimming

Assuming the length of a primer is 20bp, we can remove it like this:

st trim ":20" input.fasta > output.fasta

However, primers may sometimes be incomplete or shifted, which is why tools such as Cutadapt are usually used to trim primers. Seqtool can do primer matching using the find command, followed by primer trimming with trim. The following example trims forward and reverse primers, storing the positions as attributes in sequence headers:

st find FWDPRIMER -f -R 0.1 -a fwd_end={match_end} input.fasta |
  st find REVPRIMER -f -R 0.1 -a rev_start={match_start} |
  st trim --exclusive '{attr(fwd_end)}:{attr(rev_start)}' > primer_trimmed.fasta

The intermediate output before the trim command may look like this:

>id f_end=15 r_start=24
BEFOREFWDPRIMERSEQUENCEREVPRIMERAFTER

primer_trimmed.fasta:

>id f_end=15 r_start=-15
SEQUENCE

Note: -e/--exclusive excludes the last base of the forward primer and the first base of the reverse primer.

Using coordinates from BED files

The following is equivalent to bedtools getfasta (note that the BED format is 0-based, thus the -0 option):

st trim -l coordinates.bed -0 '{meta(2)}:{meta(3)}' input.fasta > output.fasta

Instead of -0 we could also use an expression to calculate start + 1, matching the standard range coordinate system used by seqtool.

st trim -l coordinates.bed '{meta(2)+1}:{meta(3)}' input.fasta > output.fasta

Multiple ranges

The trim command can also concatenate multiple parts of the sequence:

st trim '2:5,10:1' input.fasta > output.fasta

More

This page lists examples with execution times compared to other tools.