Picking n-th spectra from a mgf file

[hsogaard]

Hello,

I would like to read a .mgf file with thousands of spectra in it, and then pick every n-th spectra in the file, to create a smaller subset of the data in a new .mgf file. I want to use mgf.write() in a for loop so that I look through the file, apply the desired logic, and then write the spectra that passes the "filter" into the new subset file.

I can read the file perfectly fine, and I can easily print every n-th spectra by indexing like this: mgfFile[n], in a for loop. However, I encounter some issues when trying to write these results to a .mgf file.

For example, taking every tenth spectra, doing something along these lines:

file = mgf.read(filePath)
nSpectra = len(file)

for i in range(nSpectra):
    if i % 10 == 0:
        mgf.write(file[i], outputFile)

Or by using with.

In other words, something like this:

open and read mgf file: 
    for each spectrum in file:
        if spectrumIndex % 10 == 0:
            mgf.write(spectrum[with matching index], outputFile)

Any help is much appreciated!
Thanks!

[mobiusklein]

mgf.write takes an Iterable over spectra, not a single spectrum as its first argument. Without seeing an error message, I have to guess this is the problem you've encountered. You can rewrite this two ways to make it work:

file = mgf.read(filePath)
nSpectra = len(file)

for i in range(nSpectra):
    if i % 10 == 0:
        mgf.write([file[i]], outputFile)

Or

file = mgf.read(filePath)
nSpectra = len(file)
mgf.write((file[i] for i in range(nSpectra) if i % 10), outputFile)

The first solves the problem by calling write and passing a list of spectra of length 1 for every spectrum you want to write.
The second solves the problem by converting your for-loop to a generator expression and passing the resulting iterator object to write

[hsogaard]

Thank you! I was missing the extra pair of brackets in the write function. The addition of these did the trick!