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codcopy.html
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<HTML>
<HEAD>
<TITLE>
EMBOSS: codcopy
</TITLE>
</HEAD>
<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">
codcopy
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Reads and writes a codon usage table
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->
<H2>
Description
</H2>
<!--
This is the main part of the document.
This is what the user looks at to find out if this program will do what he wants.
Long description.
Why it is useful.
When it should/shouldn't be used.
-->
Copies a codon usage table. This program supports all available codon
usage input and output formats. Rather than a copy utility, it is
intended as a format conversion utility so that codon usage data can
be exported to other applications that support only a single format.
<H2>
Algorithm
</H2>
<!--
Algorithms
Pseudocode/Vague description/Handwaving/web links to useful pages
-->
<H2>
Usage
</H2>
<!--
Example usage, as run from the command-line.
Many examples illustrating different behaviours is good.
-->
<b>Here is a sample session with codcopy</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>codcopy </b>
Reads and writes a codon usage table
Codon usage file: <b>Eecoli.cut</b>
Codon usage output file [eecoli.cut]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#output.1">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:
[-infile] codon Codon usage table name
[-outfile] outcodon Codon usage table name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-infile" associated qualifiers
-format1 string Data format
"-outfile" associated qualifiers
-odirectory2 string Output directory
-oformat2 string Output format specific to this data type
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>[-infile]<br>(Parameter 1)</td>
<td>Codon usage table name</td>
<td>Codon usage file in EMBOSS data path</td>
<td> </td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Codon usage table name</td>
<td>Codon usage file</td>
<td> </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 colspan=4>(none)</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 colspan=4>(none)</td>
</tr>
</table>
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->
<H2>
Input file format
</H2>
<!--
This includes example input file formats.
This should be a detailed description and example - assume
someone will want to parse this file and will want to know what
happens in unusual cases - null input, etc.
-->
<b>codcopy</b> reads any normal sequence USAs.
<p>
<H2>
Output file format
</H2>
<b>codcopy</b>
outputs a graph to the specified graphics device.
outputs a report format file. The default format is ...
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: eecoli.cut</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
#Species: Escherichia coli K12
#Division: gbbct
#Release: CUTG146
#CdsCount: 5045
#Coding GC 51.81%
#1st letter GC 58.93%
#2nd letter GC 40.69%
#3rd letter GC 55.80%
#Codon AA Fraction Frequency Number
GCA A 0.214 20.299 32456
GCC A 0.269 25.493 40761
GCG A 0.355 33.631 53773
GCT A 0.162 15.354 24549
TGC C 0.554 6.431 10283
TGT C 0.446 5.180 8282
GAC D 0.372 19.047 30454
GAT D 0.628 32.219 51514
GAA E 0.690 39.570 63268
GAG E 0.310 17.782 28431
TTC F 0.425 16.580 26510
TTT F 0.575 22.423 35852
GGA G 0.108 7.925 12671
GGC G 0.402 29.403 47013
GGG G 0.150 10.994 17578
GGT G 0.340 24.838 39714
CAC H 0.429 9.712 15529
CAT H 0.571 12.903 20630
ATA I 0.072 4.290 6860
ATC I 0.419 24.999 39971
ATT I 0.510 30.427 48649
AAA K 0.767 33.618 53752
AAG K 0.233 10.198 16305
CTA L 0.036 3.860 6172
CTC L 0.104 11.045 17660
CTG L 0.496 52.821 84455
CTT L 0.104 11.051 17670
TTA L 0.131 13.913 22246
TTG L 0.129 13.727 21948
ATG M 1.000 27.778 44414
AAC N 0.551 21.611 34554
AAT N 0.449 17.633 28193
CCA P 0.192 8.524 13629
CCC P 0.125 5.531 8843
CCG P 0.524 23.235 37150
CCT P 0.159 7.045 11265
CAA Q 0.349 15.474 24742
CAG Q 0.651 28.832 46100
AGA R 0.037 2.056 3287
AGG R 0.022 1.216 1944
CGA R 0.064 3.542 5663
CGC R 0.398 22.005 35184
CGG R 0.098 5.391 8619
CGT R 0.381 21.020 33609
AGC S 0.277 16.031 25632
AGT S 0.151 8.723 13947
TCA S 0.123 7.137 11411
TCC S 0.148 8.591 13736
TCG S 0.154 8.916 14256
TCT S 0.147 8.507 13601
ACA T 0.131 7.035 11248
ACC T 0.435 23.362 37354
ACG T 0.268 14.371 22977
ACT T 0.166 8.922 14265
GTA V 0.154 10.883 17400
GTC V 0.215 15.221 24336
GTG V 0.371 26.253 41976
GTT V 0.260 18.394 29410
TGG W 1.000 15.303 24468
TAC Y 0.429 12.243 19576
TAT Y 0.571 16.326 26103
TAA * 0.642 2.025 3237
TAG * 0.072 0.228 365
TGA * 0.286 0.902 1443
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None
<H2>
Notes
</H2>
<!--
Restrictions.
Interesting behaviour.
Useful things you can do with this program.
-->
None.
<H2>
References
</H2>
<!--
Bibliography for methods used.
<ol>
<li>
</ol>
-->
None.
<H2>
Warnings
</H2>
<!--
Potentially stupid things the program will let you do.
-->
None.
<H2>
Diagnostic Error Messages
</H2>
<!--
Error messages specific to this program, eg:
"FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
-->
None.
<H2>
Exit status
</H2>
<!--
Description of the exit status for various error conditions
-->
It always exits with status 0.
<H2>
Known bugs
</H2>
<!--
Bugs noted but not yet fixed.
-->
None.
<!--
<H2>
See also
</H2>
-->
<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="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="trimseq.html">trimseq</a></td>
<td>Trim ambiguous bits off the ends of 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>
<!--
Add any comments about other associated programs (to prepare
data files?) that seealso doesn't find.
-->
<H2>
Author(s)
</H2>
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
<!--
Date written and what changes have been made go in this file.
-->
<H2>
Target users
</H2>
<!--
For general users, use this text
-->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
<!--
User/developer/other comments go in this file.
-->
None
</BODY>
</HTML>