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).