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a/image_ref/utils.py +++ b/image_ref/utils.py @@ -1,3 +1,5 @@ +import os + import fastapy import matplotlib.pyplot as plt import numpy as np @@ -7,13 +9,21 @@ from analyse_diann_digestion import load_lib import matplotlib.image as mpimg import re -SPECIES = ['Citrobacter cronae', 'Citrobacter portucalensis', 'Enterobacter hormaechei', 'Klebsiella aerogenes', - 'Klebsiella variicola', 'Raoultella ornithinolytica', 'Citrobacter farmeri', 'Enterobacter asburiae', - 'Enterobacter kobei', 'Klebsiella michiganensis', 'Morganella morganii', 'Salmonella enterica', - 'Citrobacter amalonaticus', 'Citrobacter freundii', 'Enterobacter chengduensis', 'Escherichia coli', - 'Klebsiella oxytoca', 'Proteus mirabilis', 'Serratia marcescens', 'Citrobacter braakii', - 'Citrobacter koseri', 'Enterobacter cloacae', 'Hafnia alvei', 'Klebsiella pneumoniae', - 'Providencia stuartii'] +# SPECIES = [f.name for f in os.scandir('../data/processed_data_wiff/npy_image/all data') if f.is_dir()] +SPECIES = ['Enterobacter bugandensis', 'Enterobacter hormaechei', 'Enterobacter cloacae', + 'Serratia marcescens', 'Morganella morganii', 'Citrobacter freundii', 'Hafnia alvei', + 'Citrobacter amalonaticus', 'Salmonella enterica', 'Klebsiella quasipneumoniae', + 'Raoultella ornithinolytica', 'Escherichia coli', 'Hafnia paralvei', 'Citrobacter portucalensis', + 'Proteus penneri', 'Providencia stuartii', + 'Klebsiella michiganensis', 'Klebsiella variicola', 'Proteus terrae', 'Pantoea septica', + 'Proteus vulgaris', 'Proteus mirabilis', 'Klebsiella oxytoca', + 'Klebsiella aerogenes', 'Proteus columbae', + 'Citrobacter koseri', 'Enterobacter kobei', + 'Klebsiella pneumoniae', 'Pantoea agglomerans', 'Klebsiella grimontii', + 'Providencia rettgeri', + 'Citrobacter farmeri', 'Enterobacter chengduensis', 'Enterobacter ludwigii', + 'Enterobacter asburiae', 'Citrobacter braakii', 'Enterobacter roggenkampii', 'Citrobacter cronae'] + # trypsin cut after K or R (if not followed by P) @@ -72,7 +82,7 @@ def build_database_ref_peptide(): for line in f: if line != '\n': if '>' in line: - #remove new line + # remove new line line = line.replace('\n', '') # typo ?? @@ -90,19 +100,20 @@ def build_database_ref_peptide(): o = split_line[3].replace('_', ' ') else: seq = line.split(' ')[1] - #remove new lines - seq = seq.replace('\n','') + # remove new lines + seq = seq.replace('\n', '') l.append({'Sequence': seq, 'Protein code': prot, 'Error treshold': err, 'Prevalance': prev, 'Specie': spe, 'Genus': gen, 'Family': fam, 'Order': o}) df = pd.DataFrame(l) return df.drop_duplicates() -def compute_common_peptide(df_path,species): + +def compute_common_peptide(df_path, species): df = pd.read_csv(df_path) df_filter = df[df['Specie'].isin(species)] - df_filter = df_filter[['Sequence','Specie']].drop_duplicates() + df_filter = df_filter[['Sequence', 'Specie']].drop_duplicates() df_filter['Count'] = df_filter.groupby('Sequence')['Sequence'].transform('count') - df_count = df_filter[['Sequence','Count']].drop_duplicates() + df_count = df_filter[['Sequence', 'Count']].drop_duplicates() return df_count @@ -126,7 +137,9 @@ def build_ref_image_from_diann(path_parqet, ms1_end_mz, ms1_start_mz, bin_mz, ma return im -def build_ref_image_from_diann_global(path_parqet, target_seq, ms1_end_mz, ms1_start_mz, bin_mz, max_cycle, min_rt=None, max_rt=None): + +def build_ref_image_from_diann_global(path_parqet, target_seq, ms1_end_mz, ms1_start_mz, bin_mz, max_cycle, min_rt=None, + max_rt=None): df = load_lib(path_parqet) df = df[['Stripped.Sequence', 'Precursor.Charge', 'RT', 'Precursor.Mz']] df = df[df['Stripped.Sequence'].isin(target_seq)] @@ -151,29 +164,32 @@ def build_ref_image_from_diann_global(path_parqet, target_seq, ms1_end_mz, ms1_s if __name__ == '__main__': # df = build_database_ref_peptide() # df.to_csv("dataset_species_ref_peptides.csv", index=False) - # #Write fasta file + # Write fasta file # with open('fasta/optimal peptide set/gobal_peptide_set.fasta', "w") as f: - # for spe in SPECIES: - # df_spe = df[df['Specie']==spe] - # spe_list = df_spe['Sequence'].drop_duplicate().to_list() - # if not spe_list: - # print('Empty : ',spe) - # for pep in spe_list : - # f.write(pep) - - df_count = compute_common_peptide("dataset_species_ref_peptides.csv", SPECIES) - + # df_spe = df[df['Specie'].isin(SPECIES)] + # spe_list = df_spe['Sequence'].drop_duplicates().to_list() # - #Create ref img - # df_full = load_lib( - # 'fasta/full proteom/steigerwaltii variants/uniparc_proteome_UP000033376_2025_03_14.predicted.parquet') - # min_rt = df_full['RT'].min() - # max_rt = df_full['RT'].max() + # for pep in spe_list : + # print(pep) + # f.write(pep+'\n') + # + # df_count = compute_common_peptide("dataset_species_ref_peptides.csv", SPECIES) + # - # for spe in SPECIES: - # im = build_ref_image_from_diann( - # 'fasta/optimal peptide set/' + spe + '.parquet', ms1_end_mz=1250, - # ms1_start_mz=350, bin_mz=1, max_cycle=663, min_rt=min_rt, max_rt=max_rt) - # plt.clf() - # mpimg.imsave('img_ref/' + spe + '.png', im) - # np.save(spe + '.npy', im) + # Create ref img + df_full = load_lib( + 'fasta/full proteom/steigerwaltii variants/uniparc_proteome_UP000033376_2025_03_14.predicted.parquet') + min_rt = df_full['RT'].min() + max_rt = df_full['RT'].max() + + df = pd.read_csv("dataset_species_ref_peptides.csv") + + for spe in SPECIES: + print(spe) + df_spe = df[df['Specie'] == spe] + im = build_ref_image_from_diann_global( + 'fasta/global_peptide_list.parquet', target_seq=df_spe['Sequence'].to_list(), ms1_end_mz=1250, + ms1_start_mz=350, bin_mz=1, max_cycle=663, min_rt=min_rt, max_rt=max_rt) + plt.clf() + mpimg.imsave('img_ref/' + spe + '.png', im) + np.save('img_ref/' + spe + '.npy', im)