libsize17.py

 #SRMColliderMetabo
from srmcollidermetabo import *
import sys

fileid = sys.argv[1]

allcomp, spectra = read(compounds = 'comp_df17.pkl', spectra = 'spec_df17.pkl')
compounds_filt_all, spectra_filt_all = filter_comp(compounds_filt=allcomp, spectra=spectra)

sizes = [1000,2000,3000,4000,5000,6000,7000,8000,9000]

for size in sizes:
    #random subsample of queries
    compounds_filt = compounds_filt_all.sample(n=size, replace=False)
    spectra_filt = spectra_filt_all.loc[spectra_filt_all['mol_id'].isin(compounds_filt.mol_id)]

    ms1_25 = method_profiler(compounds_filt = compounds_filt.copy(), spectra_filt=spectra_filt.copy(), change=0, ppm=25, change_q3=0, ppm_q3=0, top_n=0.1, mol_id=0, uis_num=0, q3=False)
    ms1_25.to_csv("/home/shantham/scratch/ms1_25_"+str(size)+"_"+fileid+"_609nist17.csv")

    mrm_7_7_3 = method_profiler(compounds_filt = compounds_filt.copy(), spectra_filt=spectra_filt.copy(),change=0.7, ppm=0, change_q3=0.7, ppm_q3=0, top_n=0.1, mol_id=0, uis_num=3, q3=True)
    mrm_7_7_3.to_csv("/home/shantham/scratch/mrm_7_7_3_"+str(size)+"_"+fileid+"_609nist17.csv")

    swath_25da_25_3 = method_profiler(compounds_filt = compounds_filt.copy(), spectra_filt=spectra_filt.copy(), change=25, ppm=0, change_q3=0, ppm_q3=25, top_n=0.1, mol_id=0, uis_num=3, q3=True)
    swath_25da_25_3.to_csv("/home/shantham/scratch/swath_25da_25_3_"+str(size)+"_"+fileid+"_609nist17.csv")

    swath_25_25_3 = method_profiler(compounds_filt = compounds_filt.copy(), spectra_filt=spectra_filt.copy(), change=0, ppm=25, change_q3=0, ppm_q3=25, top_n=0.1, mol_id=0, uis_num=3, q3=True)
    swath_25_25_3.to_csv("/home/shantham/scratch/swath_25_25_3_"+str(size)+"_"+fileid+"_609nist17.csv")