| trimseq

## Function

Trim ambiguous bits off the ends of sequences

## Description

This program is used to tidy up the ends of sequences, removing all the bits that you would really rather were not published.

Specifically, it:

- removes all gap characters from the ends.
- removes X's and N's (in nucleic sequences) from the ends.
- optionally removes *'s from the ends
- optionally removes IUPAC ambiguity codes from the ends (B and Z in proteins, M,R,W,S,Y,K,V,H,D and B in nucleic sequences)

It then optionally trims off poor quality regions from the end, using a threshold percentage of unwanted characters in a window which is moved along the sequence from the ends. The unwanted characters which are used are X's and N's (in nucleic sequences), optionally *'s, and optionally IUPAC ambiguity codes.

The program stops trimming the ends when the percentage of unwanted characters in the moving window drops below the threshold percentage.

Thus if the window size is set to 1 and the percentage threshold is 100, no further poor quality regions will be removed. If the window size is set to 5 and the percentage threshold is 40 then the sequence AAGCTNNNNATT will be trimmed to AAGCT, while AAGCTNATT or AAGCTNNNNATTT will not be trimmed as less than 40% of the last 5 characters are N's.

After trimming these poor quality regions, it will again then trim off any dangling gap characters from the ends .

## Usage

Tidy up the sequence ends, stopping at the first wanted code

    % trimseq xyz.seq xyz_clean.seq -window 1 -percent 100

Tidy up the sequence ends, removing poor bits at the ends

    % trimseq xyz.seq xyz_clean.seq -window 5 -percent 40

Tidy up the sequence ends, removing very poor bits at the ends

    % trimseq xyz.seq xyz_clean.seq -window 20 -percent 80

Tidy up the sequence ends, removing even maginally poor bits at the ends

    % trimseq xyz.seq xyz_clean.seq -window 20 -percent 10

Tidy up the sequence ends, removing poor bits including ambiguity codes

    % trimseq xyz.seq xyz_clean.seq -window 20 -percent 50 -strict

Tidy up the sequence ends, removing asterisks from a protein end

    % trimseq xyz.seq xyz_clean.seq -window 1 -percent 100 -star

Tidy up the sequence ends, removing poor bits at only the left end

    % trimseq xyz.seq xyz_clean.seq -window 20 -percent 50 -noright

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outseq]            seqoutall  Output sequence(s) USA

       Optional qualifiers:
       -window             integer    This determines the size of the region that
                                      is considered when deciding whether the
                                      percentage of ambiguity is greater than the
                                      threshold. A value of 5 means that a region
                                      of 5 letters in the sequence is shifted
                                      along the sequence from the ends and
                                      trimming is done only if there is a greater
                                      or equal percentage of ambiguity than the
                                      threshold percentage.
       -percent            float      This is the threshold of the percentage
                                      ambiguity in the window required in order to
                                      trim a sequence.
       -strict             boolean    In nucleic sequences, trim off not only N's
                                      and X's, but also the nucleotide IUPAC
                                      ambiguity codes M, R, W, S, Y, K, V, H, D
                                      and B. In protein sequences, trim off not
                                      only X's but also B and Z.
       -star               boolean    In protein sequences, trim off not only X's,
                                      but also the *'s

       Advanced qualifiers:
       -[no]left           boolean    Trim at the start
       -[no]right          boolean    Trim at the end

       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outseq" related qualifiers
       -osformat2           string     Output seq format
       -osextension2        string     File name extension
       -osname2             string     Base file name
       -osdirectory2        string     Output directory
       -osdbname2           string     Database name to add
       -ossingle2           boolean    Separate file for each entry
       -oufo2               string     UFO features
       -offormat2           string     Features format
       -ofname2             string     Features file name
       -ofdirectory2        string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning             boolean    Report warnings
       -error               boolean    Report errors
       -fatal               boolean    Report fatal errors
       -die                 boolean    Report deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format
Optional qualifiers | Allowed values | Default
-window | This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage. | Any integer value | 1
-percent | This is the threshold of the percentage ambiguity in the window required in order to trim a sequence. | Any numeric value | 100.0
-strict | In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z. | Boolean value Yes/No | No
-star | In protein sequences, trim off not only X's, but also the *'s | Boolean value Yes/No | No
Advanced qualifiers | Allowed values | Default
-[no]left | Trim at the start | Boolean value Yes/No | Yes
-[no]right | Trim at the end | Boolean value Yes/No | Yes

## Input file format

Normal sequence.

## Output file format

Normal sequence file.

## Data files

None.

## Notes

If you use the '-star' qualifier and set the window size to greater than 1, you may trim bits of sequence with internal *'s. This may not be what you expected.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None noted.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
skipseq | Reads and writes (returns) sequences, skipping the first few
splitter | Split a sequence into (overlapping) smaller sequences
trimest | Trim poly-A tails off EST sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments