Processing your data

Running raw2feats.py

To process your data, navigate to the directory containing your summary and sequence files using the command line. If this directory does not also contain your data, make sure to specify that in the DATA_DIRECTORY attribute in the summary file. Then, type

python /path/to/raw2feats.py -i /path/to/input/directory

Alternatively, if you want to specify a different output directory than the default, you can type

python /path/to/raw2feats.py -i /path/to/input/directory -o /full/path/to/output/directory

Note that you must have raw2feats.py, SummaryParserMtab.py, and preprocessingmtab.py all added to your PYTHONPATH or in the same folder.

Knowing when it’s finished

When the data is finished processing, you should see [[Processing mzML files]] Done. print to screen.

Saving the outputs to files

Using Windows DOS command line, you can save the stdout (i.e. anything that is spit out by any of the python codes) by piping your command to a file name using >. You can also save the outputs of the calls to the R files using 2>. For example, the following command saves the python outputs to out1.txt and the R outputs to out2.txt

python /path/to/raw2feats.py -i /path/to/input/directory > out1.txt 2> out2.txt

Saving outputs on UNIX command line should be straightforward (but to be honest I wrote most of this code back in the dark ages before I got a Mac so I haven’t tested it out).