| Previous changeset 63:b8cbc2122d55 (2020-03-16) Next changeset 65:a61733753aec (2020-03-16) |
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Commit message:
Uploaded |
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modified:
Marea/marea.py |
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| diff -r b8cbc2122d55 -r 53b4fca5bdf9 Marea/marea.py --- a/Marea/marea.py Mon Mar 16 07:45:59 2020 -0400 +++ b/Marea/marea.py Mon Mar 16 07:47:12 2020 -0400 |
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| @@ -537,6 +537,36 @@ warning('Warning: wrong format rule in ' + str(err_rules) + '\n') return (split_rules, list(set(tmp_gene_in_rule))) +def make_recon(data): + try: + import cobra as cb + import warnings + with warnings.catch_warnings(): + warnings.simplefilter('ignore') + recon = cb.io.read_sbml_model(data) + react = recon.reactions + rules = [react[i].gene_reaction_rule for i in range(len(react))] + ids = [react[i].id for i in range(len(react))] + except cb.io.sbml.CobraSBMLError: + try: + data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('') + if len(data.columns) < 2: + sys.exit('Execution aborted: wrong format of '+ + 'custom datarules\n') + if not len(data.columns) == 2: + warning('Warning: more than 2 columns in custom datarules.\n' + + 'Extra columns have been disregarded\n') + ids = list(data.iloc[:, 0]) + rules = list(data.iloc[:, 1]) + except pd.errors.EmptyDataError: + sys.exit('Execution aborted: wrong format of custom datarules\n') + except pd.errors.ParserError: + sys.exit('Execution aborted: wrong format of custom datarules\n') + split_rules, tmp_genes = do_rules(rules) + gene_in_rule = {} + for i in tmp_genes: + gene_in_rule[i] = 'ok' + return (ids, split_rules, gene_in_rule) ############################ gene ############################################# @@ -636,6 +666,7 @@ if comparison == "manyvsmany": for i, j in it.combinations(class_pat.keys(), 2): + tmp = {} count = 0 max_F_C = 0 @@ -671,6 +702,10 @@ renderPDF.drawToFile(svg2rlg(file_svg), file_pdf) if not create_svg: + #Ho utilizzato il file svg per generare il pdf, + #ma l'utente non ne ha richiesto il ritorno, quindi + #lo elimino + os.remove('result/' + i + '_vs_' + j + ' (SVG Map).svg') elif comparison == "onevsrest": for single_cluster in class_pat.keys(): @@ -704,8 +739,8 @@ tmp_csv.to_csv(tab, sep = '\t', index = False, header = header) if create_svg or create_pdf: - if args.custom_rules == 'false' or (args.custom_rules == 'true' - and args.custom_map != ''): + if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom' + and args.yes_no == 'yes'): fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C) file_svg = 'result/' + single_cluster + '_vs_ rest (SVG Map).svg' with open(file_svg, 'wb') as new_map: @@ -721,10 +756,6 @@ elif comparison == "onevsmany": for i, j in it.combinations(class_pat.keys(), 2): - if i != control and j != control: - continue - if i == control and j == control: - continue tmp = {} count = 0 max_F_C = 0 @@ -747,8 +778,8 @@ tmp_csv.to_csv(tab, sep = '\t', index = False, header = header) if create_svg or create_pdf: - if args.custom_rules == 'false' or (args.custom_rules == 'true' - and args.custom_map != ''): + if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom' + and args.yes_no == 'yes'): fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C) file_svg = 'result/' + i + '_vs_' + j + ' (SVG Map).svg' with open(file_svg, 'wb') as new_map: @@ -760,6 +791,10 @@ renderPDF.drawToFile(svg2rlg(file_svg), file_pdf) if not create_svg: + #Ho utilizzato il file svg per generare il pdf, + #ma l'utente non ne ha richiesto il ritorno, quindi + #lo elimino + os.remove('result/' + i + '_vs_' + j + ' (SVG Map).svg') @@ -777,6 +812,9 @@ if os.path.isdir('result') == False: os.makedirs('result') + + if args.custom_rules == 'true': + ids, rules, gene_in_rule = make_recon(args.custom_rule) class_pat = {} |