| 184 |
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emerge, the code that interfaces with the instrument software need not |
| 185 |
|
change. |
| 186 |
|
<P> |
| 187 |
+ |
<quote> |
| 188 |
+ |
<b>NOTE!</b> |
| 189 |
+ |
<P> |
| 190 |
+ |
The vendor software (Analyst for .wiff |
| 191 |
+ |
files, Data Explorer for .t2d files) be installed on the same computer |
| 192 |
+ |
as <b>PyMsXML</b>. These binary formats cannot be read without the |
| 193 |
+ |
vendor support libraries. |
| 194 |
+ |
</quote> |
| 195 |
+ |
<P> |
| 196 |
|
<h3>Installation</h3> |
| 197 |
|
<P> |
| 198 |
|
<ol> |
| 231 |
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</code> |
| 232 |
|
<P> |
| 233 |
|
<li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A |
| 234 |
< |
href="http://bioinformatics.org/project/filelist.php?group_id=701">Download |
| 234 |
> |
href="http://www.umiacs.umd.edu/~nedwards/research/downloads/PyMsXML.zip">Download |
| 235 |
|
<b>PyMsXML</b></A>. After unzipping <b>PyMsXML</b>, edit the file pymsxml.cmd to |
| 236 |
|
point to your Python installation (usually C:\Python24\python.exe) |
| 237 |
|
and your <b>PyMsXML</b> installation. |
| 250 |
|
<dl> |
| 251 |
|
<dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt> |
| 252 |
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<dd>Valid <i>raw-format</i> values: <tt>wiff</tt>, <tt>qstar</tt>, <tt>t2d</tt>, <tt>ab4700</tt>, <tt>voyager</tt>, <tt>mariner</tt>, <tt>mzXML</tt>. Optional if <i>raw-spectra-data-file</i> ends in <tt>.wiff</tt>, <tt>.t2m</tt>, or <tt>.mzXML</tt>. |
| 244 |
– |
</dd> |
| 253 |
|
<P> |
| 254 |
|
<dt>-X <i>xml-format</i>, --xmlformat <i>xml-format</i></dt> |
| 255 |
|
<dd>Valid <i>xml-format</i> values: <tt>mzXML</tt> (ISB), <tt>mzData</tt> (HUPO). Optional if <i>output-file</i> ends in <tt>.mzXML</tt> or <tt>.mzData</TT>. |
| 248 |
– |
</dd> |
| 256 |
|
<P> |
| 257 |
|
<dt>-o <i>output-file</i>, --output <i>output-file</i></dt> |
| 258 |
|
<dd>Name of output file. If omitted, and <i>xml-format</i> is supplied, then the output file is inferred by changing the file extention of <i>raw-spectra-data-file</i> to <i>xml-format</i>. |
| 252 |
– |
</dd> |
| 259 |
|
<P> |
| 260 |
|
<dt>-p <i>ms-levels</i>, --peaks <i>ms-levels</i></dt> |
| 261 |
|
<dd> Apply (vendor library) peak detetion to spectra with level in <i>ms-levels</i> (comma separated). QStar (MS/MS spectra only) raw format, 4700 raw format only. Default: 2. |
| 256 |
– |
</dd> |
| 262 |
|
<P> |
| 263 |
|
<dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> <dd> |
| 264 |
|
Filter output scans by their meta-data. Filters are specified as a |
| 268 |
|
<tt>eq</tt>, <tt>ne</tt>, <tt>lt</tt>, <tt>le</tt>, <tt>gt</tt>, or |
| 269 |
|
<tt>ge</tt>, specifying =, ≠, <, ≤, >, and ≥ |
| 270 |
|
respectively. |
| 266 |
– |
</dd> |
| 267 |
– |
<P> |
| 268 |
– |
<dt>-V <i>xml-version</i>, --version <i>xml-version</i></dt> |
| 269 |
– |
<dd> |
| 270 |
– |
XML version. mzXML only. Valid values: <tt>2.1</tt>, <tt>2.2</tt>, and <tt>3.0</tt>. Default: <tt>3.0</tt> |
| 271 |
– |
</dd> |
| 272 |
– |
<P> |
| 273 |
– |
<dt>-z, --compress_peaks</dt> |
| 274 |
– |
<dd> Compress mzXML peaks data using zlib. mzXML version ≥ 3.0 only. Default: False. |
| 275 |
– |
</dd> |
| 271 |
|
<P> |
| 272 |
|
<dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt> |
| 273 |
< |
<dd> Compress output file. Valid values: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>. |
| 279 |
< |
</dd> |
| 273 |
> |
<dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>. |
| 274 |
|
<P> |
| 275 |
|
<dt>-d, --debug</dt> |
| 276 |
|
<dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd> |
