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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.
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>
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207   libraries for reading ".dat" and ".t2d" files. If you have both pieces
208   of software, repeat this step for each software package. Click OK.
209   <P>
210 < <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.
210 > <li> Check the installation of COM library interfaces. If any of these
211 > tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the
212 > corresponding raw datafiles.
213   <P>
214 < For Analyst, these commands at the Pythonwin IDE command-line (copy-and-paste!) should elicit similar responses:<br>
214 > For Analyst, these commands at the Pythonwin IDE command-line
215 > (copy-and-paste!) should elicit similar responses:<br>
216   <code>
217   >>> from win32com.client import Dispatch<br>
218   >>> Dispatch('Analyst.FMANSpecData')<br>
# Line 249 | Line 249
249   <dd>
250   <dl>
251   <dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt>
252 < <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>.
252 > <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>.
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>.
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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.
262   <P>
263 < <dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt>
264 < <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.
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
265 > comma-separated list of filter tokens. Each filter token is specified
266 > as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be
267 > an attribute of the scan object. <i>comparison</i> must be one of
268 > <tt>eq</tt>, <tt>ne</tt>, <tt>lt</tt>, <tt>le</tt>, <tt>gt</tt>, or
269 > <tt>ge</tt>, specifying =, &ne;, &lt;, &le;, &gt;, and &ge;
270 > respectively.
271   <P>
272   <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
273 < <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.
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>
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284   <h3>Applied Biosystems Q-Star Spectra</h3>
285   <P>
286   The raw spectra data files for the ESI spectra from Applied
287 < Biosystems' Q-Star instruments are usually
288 < extracted as ".wiff" files. These can be opened using Applied
289 < Biosystem's Analyst or BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries to extract profile mass spectra from these files.
287 > Biosystems' Q-Star instruments are usually extracted as ".wiff"
288 > files. These can be opened using Applied Biosystem's Analyst or
289 > BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries
290 > to extract mass spectra from these files.
291   <P>
292   <P>
293   <h3>Applied Biosystems Mariner, Voyager, 4700 Spectra</h3>
# Line 289 | Line 296
296   Biosystems' Mariner, Voyager and 4700 instruments are usually
297   extracted as ".t2d" or ".dat" files. These can be opened using Applied
298   Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's
299 < support libraries to extract profile mass spectra from these
299 > support libraries to extract mass spectra from these
300   files. These file formats store very little meta-data in addition to
301   the mass spectrum. As such, additional information must be supplied in
302   a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.

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