diff --git a/feature-based-molecular-networking/feature-based-molecular-networking/input.xml b/feature-based-molecular-networking/feature-based-molecular-networking/input.xml index c5e7d6ac..a4c44686 100644 --- a/feature-based-molecular-networking/feature-based-molecular-networking/input.xml +++ b/feature-based-molecular-networking/feature-based-molecular-networking/input.xml @@ -165,13 +165,14 @@ diff --git a/feature-based-molecular-networking/test-integration-workflow/test_tasks.csv b/feature-based-molecular-networking/test-integration-workflow/test_tasks.csv index 39d9546d..e1377fee 100644 --- a/feature-based-molecular-networking/test-integration-workflow/test_tasks.csv +++ b/feature-based-molecular-networking/test-integration-workflow/test_tasks.csv @@ -20,4 +20,5 @@ d0b5249f7d69443a8adcb9e43ebcc0a2,fbmn IIN,view_all_clusters_withID d513e6923920413a89f1669b16117e1d,fbmn with mzML files,file_summary f932ba2238c04499b48c696008c33672,fbmn with IIN collapse, 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b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/reformat_quantification.py index 6c425178..03754da2 100644 --- a/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/reformat_quantification.py +++ b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/reformat_quantification.py @@ -16,6 +16,7 @@ import progenesis_formatter import mztabm_formatter import agilent_formatter +import sirius_formatter import proteosafe @@ -128,6 +129,17 @@ def main(): compound_filename_mapping = mztabm_formatter.convert_to_feature_csv(args.quantification_table, args.quantification_table_reformatted) mztabm_formatter.create_mgf(input_filenames, args.output_mgf, compound_filename_mapping, name_mangle_mapping=name_mangle_mapping) + elif args.toolname == "SIRIUS": + print("SIRIUS") + + if len(input_filenames) != 1: + print("Must input exactly 1 spectrum mgf file") + exit(1) + + input_mgf = input_filenames[0] + shutil.copyfile(input_mgf, args.output_mgf) + sirius_formatter.convert_to_feature_csv(args.quantification_table, args.quantification_table_reformatted) + # Finally, we can renormlize the output try: if args.QUANT_FILE_NORM == "RowSum": diff --git a/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/sirius_formatter.py b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/sirius_formatter.py new file mode 100644 index 00000000..a4d3af4e --- /dev/null +++ b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/sirius_formatter.py @@ -0,0 +1,32 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- + +import pandas as pd +import sys + +def convert_to_feature_csv(input_filename, output_filename): + # Transform the header to be + input_quantification = pd.read_csv(input_filename,sep=',') + + filename = list(input_quantification.columns) + append_str = ' Peak area' + rename_filename = [sub + append_str for sub in filename[3:]] + rename = filename[:3] + rename_filename + input_quantification.columns = rename + input_quantification.to_csv(output_filename,index = False) + +###function verifies that the quant table follows proper mzmine format +def validate_mzmine_output_file(quant_table_filename): + required_columns = ["row ID", "row retention time", "row m/z"] + file_open = open(quant_table_filename, 'r') + first_line = next(file_open) + + #try splitting it by comma + all_columns_list = first_line.split(",") + + #make sure the manatory headings are in the file + assert(set(required_columns).issubset(set(all_columns_list))) + +if __name__=="__main__": + # there should be obly one input file + convert_to_feature_csv(sys.argv[1], sys.argv[2]) diff --git a/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/write_description.py b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/write_description.py index fee2f0bf..afdab914 100644 --- a/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/write_description.py +++ b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/write_description.py @@ -59,8 +59,9 @@ def write_description(param_xml_filename, output_description_filename): #CITATIONS output_sentences.append('

\nCitations

\n') - output_sentences.append('For Feature-Based Molecular Networking: Nothias LF et al. Feature-based Molecular Networking in the GNPS Analysis Environment. bioRxiv 812404 (2019). https://doi.org/10.1101/812404. \n') + output_sentences.append('For Feature-Based Molecular Networking: Nothias LF, Petras D, Schmid R et al. Feature-based Molecular Networking in the GNPS Analysis Environment. bioRxiv 812404 (2019). https://doi.org/10.1101/812404. \n') output_sentences.append('

For the GNPS web-platform: Wang M et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology 34.8 (2016): 828-837. https://doi.org/10.1038/nbt.3597. \n') + output_sentences.append('

If Ion-Identity Molecular Networking was performed: Schmid R, Petras D, Nothias LF, et al. Ion Identity Molecular Networking in the GNPS Environment, BioRxiv (2020), https://doi.org/10.1101/2020.05.11.088948. \n') #PROCESSING CITATION if param_obj["QUANT_TABLE_SOURCE"][0] == "MZMINE2": @@ -81,6 +82,8 @@ def write_description(param_xml_filename, output_description_filename): output_sentences.append('

For Progenesis QI: Progenesis QI, Nonlinear Dynamics, Milford, MA, version [specify the version]. Software available at https://www.nonlinear.com/progenesis/qi/. \n') if param_obj["QUANT_TABLE_SOURCE"][0] == "MZTABM": output_sentences.append('

For mzTab-M: Hoffman et al. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomic. Analytical Chemistry 9153302-3310 (2019), https://doi.org/10.1021/acs.analchem.8b04310>. \n') + if param_obj["QUANT_TABLE_SOURCE"][0] == "SIRIUS": + output_sentences.append('

For SIRIUS: the processing was introduced in that preprint: Hoffman et al, Assigning confidence to structural annotations from mass spectra with COSMIC, BioRxiv 2021. https://www.biorxiv.org/content/10.1101/2021.03.18.435634v1. For other SIRIUS related citations, see https://boecker-lab.github.io/docs.sirius.github.io/#literature.\n') #DEREPLICATOR ifitwas used if param_obj["RUN_DEREPLICATOR"][0] == "1":