Changing decoy label from X!Tandem

[Tim Van Den Bossche]

Dear,

 

In X!Tandem and Pyteomics, the default label for labeling decoys is the “DECOY_” prefix, as indicated by the is_decoy function. I was wondering how I can change this tag to another suffix, without digging into the source code?

For example, I would like to indicate the following:

Ftf = tandem.filter(“example.t.xml”, fdr=0.01, id_decoy=”REVERSED”) # “REVERSED” is the label which is attached to all decoy fasta headers at the end of the header

 

Best,

Tim

 

[Mark Ivanov]

Dear Tim,

Thank you for pointing this issue!

Right now you can overcame it in this way:

suffix = ':reversed' # Default X!Tandem suffix

is_decoy_func = lambda x: all(prot['label'].endswith(suffix) for prot in x['protein'])

Ftf = tandem.filter(“example.t.xml”, fdr=0.01, is_decoy=is_decoy_func)

Or if you wish to use prefix:

prefix = 'Custom_decoy_'

is_decoy_func = lambda x: all(prot['label'].startswith(prefix) for prot in x['protein'])

Ftf = tandem.filter(“example.t.xml”, fdr=0.01, is_decoy=is_decoy_func)

We understand that it is not very convenient and probably will add additional options to filter function soon.

Regards,

Mark