dbiblast.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>[-dbname]<br>(Parameter 1)</td>
<td>Database name</td>
<td>Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>-directory</td>
<td>Database directory</td>
<td>Directory</td>
<td>.</td>
</tr>

<tr>
<td>-filenames</td>
<td>Wildcard database filename</td>
<td>Any string is accepted</td>
<td>Database name</td>
</tr>

<tr>
<td>-release</td>
<td>Release number</td>
<td>Any string up to 9 characters</td>
<td>0.0</td>
</tr>

<tr>
<td>-date</td>
<td>Index date</td>
<td>Date string dd/mm/yy</td>
<td>00/00/00</td>
</tr>

<tr>
<td>-seqtype</td>
<td>Sequence type</td>
<td><table><tr><td>N</td> <td><i>(nucleic)</i></td></tr><tr><td>P</td> <td><i>(protein)</i></td></tr><tr><td>?</td> <td><i>(unknown)</i></td></tr></table></td>
<td>unknown</td>
</tr>

<tr>
<td>-blastversion</td>
<td>Blast index version</td>
<td><table><tr><td>1</td> <td><i>(wublast and setdb/pressdb)</i></td></tr><tr><td>2</td> <td><i>(formatdb)</i></td></tr><tr><td>0</td> <td><i>(unknown)</i></td></tr></table></td>
<td>unknown</td>
</tr>

<tr>
<td>-outfile</td>
<td>General log output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.dbiblast</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>-fields</td>
<td>Index fields</td>
<td><table><tr><td>acc</td> <td><i>(acnum accession number index)</i></td></tr><tr><td>sv</td> <td><i>(seqvn sequence version and gi number index)</i></td></tr><tr><td>des</td> <td><i>(des description index)</i></td></tr></table></td>
<td>acc</td>
</tr>

<tr>
<td>-exclude</td>
<td>Wildcard filename(s) to exclude</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>

<tr>
<td>-sortoptions</td>
<td>Sort options, typically '-T .' to use current directory for work files and '-k 1,1' to force GNU sort to use the first field</td>
<td>Any string is accepted</td>
<td>-T . -k 1,1</td>
</tr>

<tr>
<td>-maxindex</td>
<td>Maximum index length</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>

<tr>
<td>-[no]systemsort</td>
<td>Use system sort utility</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-[no]cleanup</td>
<td>Clean up temporary files</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-sourcefile</td>
<td>Use FASTA source file</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-indexoutdir</td>
<td>Index file output directory</td>
<td>Output directory</td>
<td>.</td>
</tr>

</table>