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  <TITLE>
  EMBOSS: trimseq
  </TITLE>
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<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
trimseq
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
    Function
</H2>
Trim ambiguous bits off the ends of sequences

<H2>
    Description
</H2>


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

<p>
Specifically, it:
<ul>

<li>removes all gap characters from the ends.
<li>removes X's and N's (in nucleic sequences) from the ends.
<li>optionally removes *'s from the ends
<li>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)
</ul>
<p>
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.

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

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

<H2>
    Usage
</H2>
<b>Here is a sample session with trimseq</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>trimseq untrimmed.seq trim1.seq -window 1 -percent 100 </b>
Trim ambiguous bits off the ends of sequences

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<p>
<b>Example 2</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>trimseq untrimmed.seq trim2.seq -window 5 -percent 40 </b>
Trim ambiguous bits off the ends of sequences

</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>
<p>
<b>Example 3</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>trimseq untrimmed.seq trim3.seq -window 5 -percent 50 </b>
Trim ambiguous bits off the ends of sequences

</pre></td></tr></table><p>
<p>
<a href="#output.3">Go to the output files for this example</a><p><p>
<p>
<b>Example 4</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>trimseq untrimmed.seq trim4.seq -window 5 -percent 50 -strict </b>
Trim ambiguous bits off the ends of sequences

</pre></td></tr></table><p>
<p>
<a href="#output.4">Go to the output files for this example</a><p><p>
<p>
<b>Example 5</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>trimseq untrimmed.seq trim5.seq -window 5 -percent 50 -strict -noright </b>
Trim ambiguous bits off the ends of sequences

</pre></td></tr></table><p>
<p>
<a href="#output.5">Go to the output files for this example</a><p><p>

<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [<sequence>.<format>] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers:
   -window             integer    [1] 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)
   -percent            float      [100.0] This is the threshold of the
                                  percentage ambiguity in the window required
                                  in order to trim a sequence. (Any numeric
                                  value)
   -strict             boolean    [N] 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    [N] In protein sequences, trim off not only
                                  X's, but also the *'s

   Advanced (Unprompted) qualifiers:
   -[no]left           boolean    [Y] Trim at the start
   -[no]right          boolean    [Y] Trim at the end

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -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
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated 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 standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -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 dying program messages

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>(Gapped) sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>[-outseq]<br>(Parameter 2)</td>
<td>Sequence set(s) filename and optional format (output USA)</td>
<td>Writeable sequence(s)</td>
<td><i>&lt;*&gt;</i>.<i>format</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-window</td>
<td>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.</td>
<td>Any integer value</td>
<td>1</td>
</tr>

<tr>
<td>-percent</td>
<td>This is the threshold of the percentage ambiguity in the window required in order to trim a sequence.</td>
<td>Any numeric value</td>
<td>100.0</td>
</tr>

<tr>
<td>-strict</td>
<td>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.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-star</td>
<td>In protein sequences, trim off not only X's, but also the *'s</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-[no]left</td>
<td>Trim at the start</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-[no]right</td>
<td>Trim at the end</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

</table>


<H2>
    Input file format
</H2>
Normal sequence.

<p>

<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: untrimmed.seq</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
&gt;myseq
...ttyyyctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttca.gnntcynnnnnn</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>


Normal sequence file.
<p>

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: trim1.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;myseq
ttyyyctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttca-gnntcy
</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: trim2.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;myseq
ttyyyctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttca-g
</pre>
</td></tr></table><p>

<a name="output.3"></a>
<h3>Output files for usage example 3</h3>
<p><h3>File: trim3.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;myseq
ttyyyctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttca-gnntcy
</pre>
</td></tr></table><p>

<a name="output.4"></a>
<h3>Output files for usage example 4</h3>
<p><h3>File: trim4.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;myseq
ctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagctc
tttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcccag
atcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcctg
gcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgact
accctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgct
ggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagaca
ggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccaccttt
ggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctctaa
taaaaaagccacttagttca-gnntc
</pre>
</td></tr></table><p>

<a name="output.5"></a>
<h3>Output files for usage example 5</h3>
<p><h3>File: trim5.seq</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&gt;myseq
ctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagctc
tttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcccag
atcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcctg
gcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgact
accctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgct
ggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagaca
ggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccaccttt
ggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctctaa
taaaaaagccacttagttca-gnntcynnnnnn
</pre>
</td></tr></table><p>

<H2>
    Data files
</H2>

None.
	
<H2>
    Notes
</H2>


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.

<H2>
    References
</H2>


None.

<H2>
    Warnings
</H2>


None.

<H2>
    Diagnostic Error Messages
</H2>


None.

<H2>
    Exit status
</H2>


It always exits with status 0.

<H2>
    Known bugs
</H2>


None noted.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="biosed.html">biosed</a></td>
<td>Replace or delete sequence sections</td>
</tr>

<tr>
<td><a href="codcopy.html">codcopy</a></td>
<td>Reads and writes a codon usage table</td>
</tr>

<tr>
<td><a href="cutseq.html">cutseq</a></td>
<td>Removes a specified section from a sequence</td>
</tr>

<tr>
<td><a href="degapseq.html">degapseq</a></td>
<td>Removes gap characters from sequences</td>
</tr>

<tr>
<td><a href="descseq.html">descseq</a></td>
<td>Alter the name or description of a sequence</td>
</tr>

<tr>
<td><a href="entret.html">entret</a></td>
<td>Reads and writes (returns) flatfile entries</td>
</tr>

<tr>
<td><a href="extractalign.html">extractalign</a></td>
<td>Extract regions from a sequence alignment</td>
</tr>

<tr>
<td><a href="extractfeat.html">extractfeat</a></td>
<td>Extract features from a sequence</td>
</tr>

<tr>
<td><a href="extractseq.html">extractseq</a></td>
<td>Extract regions from a sequence</td>
</tr>

<tr>
<td><a href="listor.html">listor</a></td>
<td>Write a list file of the logical OR of two sets of sequences</td>
</tr>

<tr>
<td><a href="makenucseq.html">makenucseq</a></td>
<td>Creates random nucleotide sequences</td>
</tr>

<tr>
<td><a href="makeprotseq.html">makeprotseq</a></td>
<td>Creates random protein sequences</td>
</tr>

<tr>
<td><a href="maskfeat.html">maskfeat</a></td>
<td>Mask off features of a sequence</td>
</tr>

<tr>
<td><a href="maskseq.html">maskseq</a></td>
<td>Mask off regions of a sequence</td>
</tr>

<tr>
<td><a href="newseq.html">newseq</a></td>
<td>Type in a short new sequence</td>
</tr>

<tr>
<td><a href="noreturn.html">noreturn</a></td>
<td>Removes carriage return from ASCII files</td>
</tr>

<tr>
<td><a href="notseq.html">notseq</a></td>
<td>Exclude a set of sequences and write out the remaining ones</td>
</tr>

<tr>
<td><a href="nthseq.html">nthseq</a></td>
<td>Writes one sequence from a multiple set of sequences</td>
</tr>

<tr>
<td><a href="pasteseq.html">pasteseq</a></td>
<td>Insert one sequence into another</td>
</tr>

<tr>
<td><a href="revseq.html">revseq</a></td>
<td>Reverse and complement a sequence</td>
</tr>

<tr>
<td><a href="seqret.html">seqret</a></td>
<td>Reads and writes (returns) sequences</td>
</tr>

<tr>
<td><a href="seqretsplit.html">seqretsplit</a></td>
<td>Reads and writes (returns) sequences in individual files</td>
</tr>

<tr>
<td><a href="skipseq.html">skipseq</a></td>
<td>Reads and writes (returns) sequences, skipping first few</td>
</tr>

<tr>
<td><a href="splitter.html">splitter</a></td>
<td>Split a sequence into (overlapping) smaller sequences</td>
</tr>

<tr>
<td><a href="trimest.html">trimest</a></td>
<td>Trim poly-A tails off EST sequences</td>
</tr>

<tr>
<td><a href="union.html">union</a></td>
<td>Reads sequence fragments and builds one sequence</td>
</tr>

<tr>
<td><a href="vectorstrip.html">vectorstrip</a></td>
<td>Strips out DNA between a pair of vector sequences</td>
</tr>

<tr>
<td><a href="yank.html">yank</a></td>
<td>Reads a sequence range, appends the full USA to a list file</td>
</tr>

</table>

<H2>
    Author(s)
</H2>
Gary Williams (gwilliam&nbsp;&copy;&nbsp;rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK



<H2>
    History
</H2>


<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.


<H2>
    Comments
</H2>
None

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