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184   emerge, the code that interfaces with the instrument software need not
185   change.
186   <P>
187 <b>PyMsXML</b> does no processing of the spectra, the output spectra
188 are as close to the raw profile data as is possible. In particular, no
189 peak detection is done for MS/MS spectra. This option may be added in
190 the future.
191 <P>
192 <b>PyMsXML</b> is <i>pre-beta</i> quality software - it may or may not
193 work reliably for you. In particular, the XML formats are in some
194 flux, and the output for ".t2d" and ".dat" files is missing much of
195 the meta-data required for fully compliant mzXML or mzData
196 XML. Further, the mzData XML format output is not as well tested as it
197 could be.
198 <P>
187   <h3>Installation</h3>
188   <P>
189   <ol>
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198   libraries for reading ".dat" and ".t2d" files. If you have both pieces
199   of software, repeat this step for each software package. Click OK.
200   <P>
201 < <li> Check the installation of COM library interfaces. If any of these tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the corresponding raw datafiles.
201 > <li> Check the installation of COM library interfaces. If any of these
202 > tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the
203 > corresponding raw datafiles.
204   <P>
205 < For Analyst, these commands at the Pythonwin IDE command-line (copy-and-paste!) should elicit similar responses:<br>
205 > For Analyst, these commands at the Pythonwin IDE command-line
206 > (copy-and-paste!) should elicit similar responses:<br>
207   <code>
208   >>> from win32com.client import Dispatch<br>
209   >>> Dispatch('Analyst.FMANSpecData')<br>
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240   <dd>
241   <dl>
242   <dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt>
243 < <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>. Optional if <i>raw-spectra-data-file</i> ends in <tt>.wiff</tt> or <tt>.t2m</tt>.
243 > <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   <P>
245   <dt>-X <i>xml-format</i>, --xmlformat <i>xml-format</i></dt>
246   <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>.
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251   <dt>-p <i>ms-levels</i>, --peaks <i>ms-levels</i></dt>
252   <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.
253   <P>
254 < <dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt>
255 < <dd> Filter output scans by their meta-data. Filters are specified as a comma-separated list of filter tokens. Each filter token is specified as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be an attribute of the scan object. <i>comparison</i> must be one of <tt>eq</tt>,<tt>ne</tt>,<tt>lt</tt>,<tt>le</tt>,<tt>gt</tt>, or <tt>ge</tt>, specifying =, !=, &lt;, &lt;=, &gt;, and &gt;= respectively.
254 > <dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> <dd>
255 > Filter output scans by their meta-data. Filters are specified as a
256 > comma-separated list of filter tokens. Each filter token is specified
257 > as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be
258 > an attribute of the scan object. <i>comparison</i> must be one of
259 > <tt>eq</tt>, <tt>ne</tt>, <tt>lt</tt>, <tt>le</tt>, <tt>gt</tt>, or
260 > <tt>ge</tt>, specifying =, &ne;, &lt;, &le;, &gt;, and &ge;
261 > respectively.
262   <P>
263   <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
264 < <dd> Compress output file. Valid options <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>. <br>Note: PyMsXML will automatically detect input files with extension <tt>.gz</tt> as compressed with gzip.
264 > <dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
265   <P>
266   <dt>-d, --debug</dt>
267   <dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd>
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275   <h3>Applied Biosystems Q-Star Spectra</h3>
276   <P>
277   The raw spectra data files for the ESI spectra from Applied
278 < Biosystems' Q-Star instruments are usually
279 < extracted as ".wiff" files. These can be opened using Applied
280 < Biosystem's Analyst or BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries to extract profile mass spectra from these files.
278 > Biosystems' Q-Star instruments are usually extracted as ".wiff"
279 > files. These can be opened using Applied Biosystem's Analyst or
280 > BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries
281 > to extract mass spectra from these files.
282   <P>
283   <P>
284   <h3>Applied Biosystems Mariner, Voyager, 4700 Spectra</h3>
# Line 289 | Line 287
287   Biosystems' Mariner, Voyager and 4700 instruments are usually
288   extracted as ".t2d" or ".dat" files. These can be opened using Applied
289   Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's
290 < support libraries to extract profile mass spectra from these
290 > support libraries to extract mass spectra from these
291   files. These file formats store very little meta-data in addition to
292   the mass spectrum. As such, additional information must be supplied in
293   a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.

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