prettyplot.itable

emboss的linux版本的源代码

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

<tr>
<td>-graph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
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<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>-matrixfile</td>
<td>This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.</td>
<td>Comparison matrix file in EMBOSS data path</td>
<td>EBLOSUM62 for protein<br>EDNAFULL for DNA</td>
</tr>

<tr>
<td>-residuesperline</td>
<td>The number of residues to be displayed on each line</td>
<td>Any integer value</td>
<td>50</td>
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<tr>
<td>-resbreak</td>
<td>Residues before a space</td>
<td>Integer 1 or more</td>
<td>Same as -residuesperline to give no breaks</td>
</tr>

<tr>
<td>-[no]ccolours</td>
<td>Colour residues by their consensus value.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-cidentity</td>
<td>Colour to display identical residues (RED)</td>
<td>Any string is accepted</td>
<td>RED</td>
</tr>

<tr>
<td>-csimilarity</td>
<td>Colour to display similar residues (GREEN)</td>
<td>Any string is accepted</td>
<td>GREEN</td>
</tr>

<tr>
<td>-cother</td>
<td>Colour to display other residues (BLACK)</td>
<td>Any string is accepted</td>
<td>BLACK</td>
</tr>

<tr>
<td>-docolour</td>
<td>Colour residues by table oily, amide etc.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-shade</td>
<td>Set to BPLW for normal shading
(black, pale, light, white)
so for pair = 1.5,1.0,0.5 and shade = BPLW
Residues score Colour
1.5 or over... BLACK (B)
1.0 to 1.5 ... BROWN (P)
0.5 to 1.0 ... WHEAT (L)
under 0.5 .... WHITE (W)
The only four letters allowed are BPLW, in any order.</td>
<td>Any string up to 4 characters, matching regular expression /^([BPLW]{4})?$/</td>
<td><i>An empty string is accepted</i></td>
</tr>

<tr>
<td>-pair</td>
<td>Values to represent identical similar related</td>
<td>List of floating point numbers</td>
<td>1.5,1.0,0.5</td>
</tr>

<tr>
<td>-identity</td>
<td>Only match those which are identical in all sequences.</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>

<tr>
<td>-[no]box</td>
<td>Display prettyboxes</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-boxcol</td>
<td>Colour the background in the boxes</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-boxcolval</td>
<td>Colour to be used for background. (GREY)</td>
<td>Any string is accepted</td>
<td>GREY</td>
</tr>

<tr>
<td>-[no]name</td>
<td>Display the sequence names</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-maxnamelen</td>
<td>Margin size for the sequence name.</td>
<td>Any integer value</td>
<td>10</td>
</tr>

<tr>
<td>-[no]number</td>
<td>Display the residue number</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-[no]listoptions</td>
<td>Display the date and options used</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-plurality</td>
<td>Plurality check value (totweight/2)</td>
<td>Any numeric value</td>
<td>Half the total sequence weighting</td>
</tr>

<tr>
<td>-consensus</td>
<td>Display the consensus</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-[no]collision</td>
<td>Allow collisions in calculating consensus</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-alternative</td>
<td>Values are 0:Normal collision check. (default)
1:Compares identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred.
2:If another residue has a greater than or equal to matching score and these do not match then a collision has occurred.
3:Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured.</td>
<td><table><tr><td>0</td> <td><i>(Normal collision check. (default))</i></td></tr><tr><td>1</td> <td><i>(Compares identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred.)</i></td></tr><tr><td>2</td> <td><i>(If another residue has a greater than or equal to matching score and these do not match then a collision has occurred.)</i></td></tr><tr><td>3</td> <td><i>(Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured.)</i></td></tr></table></td>
<td>0</td>
</tr>

<tr>
<td>-showscore</td>
<td>Print residue scores</td>
<td>Any integer value</td>
<td>-1</td>
</tr>

<tr>
<td>-portrait</td>
<td>Set page to Portrait</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 colspan=4>(none)</td>
</tr>

</table>