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184   emerge, the code that interfaces with the instrument software need not
185   change.
186   <P>
187 + <b>PyMsXML</b> is hosted at <a href="http://bioinformatics.org/project/?group_id=701">bioinformatics.org</a>.
188 + <P>
189   <quote>
190   <b>NOTE!</b>
191   <P>
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233   </code>
234   <P>
235   <li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A
236 < href="http://www.umiacs.umd.edu/~nedwards/research/downloads/PyMsXML.zip">Download
236 > href="http://bioinformatics.org/project/filelist.php?group_id=701">Download
237   <b>PyMsXML</b></A>. After unzipping <b>PyMsXML</b>, edit the file pymsxml.cmd to
238   point to your Python installation (usually C:\Python24\python.exe)
239   and your <b>PyMsXML</b> installation.
# Line 269 | Line 271
271   <tt>ge</tt>, specifying =, &ne;, &lt;, &le;, &gt;, and &ge;
272   respectively.
273   <P>
274 + <dt>-V <i>version</i>, --version <i>version</i></dt><dd>
275 +                        XML version. mzXML only. Valid options
276 +                        <tt>2.1</tt>,<tt>2.2</tt>,<tt>3.0</tt>. Default: <tt>3.0</tt>.
277 + <P>
278 + <dt>-z, --compress_peaks</dt>
279 + <dd>Compress mzXML peak data using zlib. Default: No compression of peak data. Requires mzXML version 3.0.</dd>
280 + <P>
281   <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
282   <dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
283   <P>
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305   Biosystems' Mariner, Voyager and 4700 instruments are usually
306   extracted as ".t2d" or ".dat" files. These can be opened using Applied
307   Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's
308 < support libraries to extract mass spectra from these
309 < files. These file formats store very little meta-data in addition to
310 < the mass spectrum. As such, additional information must be supplied in
311 < a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.
308 > support libraries to extract mass spectra from these files. These file
309 > formats store very little meta-data in addition to the mass
310 > spectrum. If you do not care whether or not the output data-file
311 > contains valid spot, matrix, and plate meta-data; and if your spectra
312 > are all contained in one raw datafile, then the datafile can be
313 > supplied on the command-line as <i>raw-spectra-data-file</i>. However, if you have many .dat or .t2d files, each corresponding to a MALDI spot, or if you wish to have spot, matrix, or plate meta-data populated into the output file, then see the next set of instructions.
314   <P>
315 + Plate, matrix, and spot meta-data must be supplied in
316 + a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.
317   The meta-data file is most easily constructed in Excel and saved as
318   tab-separated-values, but it can be formed by hand too, if
319   desired. Each line of the meta-data file specifies a record,
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402   C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br>
403   </code>
404   <P>
405 + Convert the Mariner ESI-CE-MALDI spectra in <tt>example3.dat</tt> to mzXML format, placing the output in the file <tt>example3.mzXML.gz</tt> (automatically gzipped):
406 + <code>
407 + C:\PyMsXML\example\dat> pymsxml.cmd -R mariner -o example3.mzXML.gz example3.dat<br>
408 + </code>
409 + <P>
410   Convert the AB4700 spectra listed in <tt>example1.t2m</tt> and <tt>example2.t2m</tt> to mzXML format, placing the output in the files <tt>example1.mzXML</tt> and <tt>example2.mzXML</tt>.<P>
411   <code>
412   C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br>

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