64
Peak alignment with the “common ion” filtering.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 | """proc.py """ import os from pyms.Experiment import load_expr from pyms.DPA.PairwiseAlignment import PairwiseAlignment, align_with_tree from pyms.DPA.Alignment import exprl2alignment #from pyms.Peak.List.IO import store_peaks # define the input experiments list exprA_codes = [ "a0806_077", "a0806_078", "a0806_079" ] exprB_codes = [ "a0806_140", "a0806_141", "a0806_142" ] # within replicates alignment parameters Dw = 2.5 # rt modulation [s] Gw = 0.30 # gap penalty # do the alignment print('Aligning expt A') expr_list = [] expr_dir = "../old demos/61a/output/" for expr_code in exprA_codes: file_name = os.path.join(expr_dir, expr_code + ".expr") expr = load_expr(file_name) expr_list.append(expr) F1 = exprl2alignment(expr_list) T1 = PairwiseAlignment(F1, Dw, Gw) A1 = align_with_tree(T1, min_peaks=2) top_ion_list = A1.common_ion() A1.write_common_ion_csv('output/area2.csv', top_ion_list) print('Aligning expt B') expr_list = [] expr_dir = "../old demos/61b/output/" for expr_code in exprB_codes: file_name = os.path.join(expr_dir, expr_code + ".expr") expr = load_expr(file_name) expr_list.append(expr) F2 = exprl2alignment(expr_list) T2 = PairwiseAlignment(F2, Dw, Gw) A2 = align_with_tree(T2, min_peaks=2) # between replicates alignment parameters Db = 10.0 # rt modulation Gb = 0.30 # gap penalty top_ion_list = A2.common_ion() A2.write_common_ion_csv('output/area1.csv', top_ion_list) print('Aligning input {1,2}') T9 = PairwiseAlignment([A1,A2], Db, Gb) A9 = align_with_tree(T9) top_ion_list = A9.common_ion() A9.write_common_ion_csv('output/area.csv', top_ion_list) |