Mercurial > repos > bimib > marea
comparison Marea/marea.py @ 48:e4235b5231e4 draft
Uploaded
| author | bimib |
|---|---|
| date | Sun, 23 Feb 2020 09:41:14 -0500 |
| parents | 3af9d394367c |
| children | 7b57a93ac594 |
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| 47:3af9d394367c | 48:e4235b5231e4 |
|---|---|
| 16 | 16 |
| 17 def process_args(args): | 17 def process_args(args): |
| 18 parser = argparse.ArgumentParser(usage = '%(prog)s [options]', | 18 parser = argparse.ArgumentParser(usage = '%(prog)s [options]', |
| 19 description = 'process some value\'s'+ | 19 description = 'process some value\'s'+ |
| 20 ' genes to create a comparison\'s map.') | 20 ' genes to create a comparison\'s map.') |
| 21 parser.add_argument('-rs', '--rules_selector', | 21 parser.add_argument('-cr', '--custom_rules', |
| 22 type = str, | 22 type = str, |
| 23 default = 'HMRcore', | 23 default = 'false', |
| 24 choices = ['HMRcore', 'Recon', 'Custom'], | 24 choices = ['true', 'false'], |
| 25 help = 'chose which type of dataset you want use') | 25 help = 'choose whether to use custom rules') |
| 26 parser.add_argument('-cr', '--custom', | 26 parser.add_argument('-cc', '--custom_rule', |
| 27 type = str, | 27 type = str, |
| 28 help='your dataset if you want custom rules') | 28 help='custom rules to use') |
| 29 parser.add_argument('-cm', '--custom_map', | |
| 30 type = str, | |
| 31 help='custom map to use') | |
| 29 parser.add_argument('-n', '--none', | 32 parser.add_argument('-n', '--none', |
| 30 type = str, | 33 type = str, |
| 31 default = 'true', | 34 default = 'true', |
| 32 choices = ['true', 'false'], | 35 choices = ['true', 'false'], |
| 33 help = 'compute Nan values') | 36 help = 'compute Nan values') |
| 53 type = str, | 56 type = str, |
| 54 help = 'input dataset') | 57 help = 'input dataset') |
| 55 parser.add_argument('-ic', '--input_class', | 58 parser.add_argument('-ic', '--input_class', |
| 56 type = str, | 59 type = str, |
| 57 help = 'sample group specification') | 60 help = 'sample group specification') |
| 58 parser.add_argument('-cm', '--custom_map', | |
| 59 type = str, | |
| 60 help = 'custom map') | |
| 61 parser.add_argument('-yn', '--yes_no', | |
| 62 type = str, | |
| 63 choices = ['yes', 'no'], | |
| 64 help = 'if make or not custom map') | |
| 65 parser.add_argument('-gs', '--generate_svg', | 61 parser.add_argument('-gs', '--generate_svg', |
| 66 type = str, | 62 type = str, |
| 67 default = 'true', | 63 default = 'true', |
| 68 choices = ['true', 'false'], | 64 choices = ['true', 'false'], |
| 69 help = 'generate svg map') | 65 help = 'generate svg map') |
| 549 warnings.simplefilter('ignore') | 545 warnings.simplefilter('ignore') |
| 550 recon = cb.io.read_sbml_model(data) | 546 recon = cb.io.read_sbml_model(data) |
| 551 react = recon.reactions | 547 react = recon.reactions |
| 552 rules = [react[i].gene_reaction_rule for i in range(len(react))] | 548 rules = [react[i].gene_reaction_rule for i in range(len(react))] |
| 553 ids = [react[i].id for i in range(len(react))] | 549 ids = [react[i].id for i in range(len(react))] |
| 554 except cb.io.sbml3.CobraSBMLError: | 550 except cb.io.sbml.CobraSBMLError: |
| 555 try: | 551 try: |
| 556 data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('') | 552 data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('') |
| 557 if len(data.columns) < 2: | 553 if len(data.columns) < 2: |
| 558 sys.exit('Execution aborted: wrong format of '+ | 554 sys.exit('Execution aborted: wrong format of '+ |
| 559 'custom datarules\n') | 555 'custom datarules\n') |
| 691 tmp_csv = tmp_csv.reset_index() | 687 tmp_csv = tmp_csv.reset_index() |
| 692 header = ['ids', 'P_Value', 'Log2(fold change)'] | 688 header = ['ids', 'P_Value', 'Log2(fold change)'] |
| 693 tmp_csv.to_csv(tab, sep = '\t', index = False, header = header) | 689 tmp_csv.to_csv(tab, sep = '\t', index = False, header = header) |
| 694 | 690 |
| 695 if create_svg or create_pdf: | 691 if create_svg or create_pdf: |
| 696 if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom' | 692 if args.custom_rules == 'false' or (args.custom_rules == 'true' |
| 697 and args.yes_no == 'yes'): | 693 and args.custom_map != ''): |
| 698 fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C) | 694 fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C) |
| 699 file_svg = 'result/' + i + '_vs_' + j + ' (SVG Map).svg' | 695 file_svg = 'result/' + i + '_vs_' + j + ' (SVG Map).svg' |
| 700 with open(file_svg, 'wb') as new_map: | 696 with open(file_svg, 'wb') as new_map: |
| 701 new_map.write(ET.tostring(core_map)) | 697 new_map.write(ET.tostring(core_map)) |
| 702 | 698 |
| 758 if not create_svg: | 754 if not create_svg: |
| 759 os.remove('result/' + single_cluster + '_vs_ rest (SVG Map).svg') | 755 os.remove('result/' + single_cluster + '_vs_ rest (SVG Map).svg') |
| 760 | 756 |
| 761 elif comparison == "onevsmany": | 757 elif comparison == "onevsmany": |
| 762 for i, j in it.combinations(class_pat.keys(), 2): | 758 for i, j in it.combinations(class_pat.keys(), 2): |
| 763 | |
| 764 if i != control and j != control: | |
| 765 print(str(control) + " " + str(i) + " " + str(j)) | |
| 766 #Se รจ un confronto fra elementi diversi dal controllo, skippo | |
| 767 continue | |
| 768 | |
| 769 print('vado') | |
| 770 tmp = {} | 759 tmp = {} |
| 771 count = 0 | 760 count = 0 |
| 772 max_F_C = 0 | 761 max_F_C = 0 |
| 773 for l1, l2 in zip(class_pat.get(i), class_pat.get(j)): | 762 for l1, l2 in zip(class_pat.get(i), class_pat.get(j)): |
| 774 try: | 763 try: |
| 821 create_svg = check_bool(args.generate_svg) | 810 create_svg = check_bool(args.generate_svg) |
| 822 create_pdf = check_bool(args.generate_pdf) | 811 create_pdf = check_bool(args.generate_pdf) |
| 823 | 812 |
| 824 if os.path.isdir('result') == False: | 813 if os.path.isdir('result') == False: |
| 825 os.makedirs('result') | 814 os.makedirs('result') |
| 826 | 815 |
| 827 if args.rules_selector == 'HMRcore': | 816 if args.custom_rules == 'true': |
| 828 recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb')) | 817 ids, rules, gene_in_rule = make_recon(args.custom_rule) |
| 829 elif args.rules_selector == 'Recon': | |
| 830 recon = pk.load(open(args.tool_dir + '/local/Recon_rules.p', 'rb')) | |
| 831 elif args.rules_selector == 'Custom': | |
| 832 ids, rules, gene_in_rule = make_recon(args.custom) | |
| 833 | 818 |
| 834 class_pat = {} | 819 class_pat = {} |
| 835 | 820 |
| 836 if args.option == 'datasets': | 821 if args.option == 'datasets': |
| 837 num = 1 | 822 num = 1 |
| 883 classes = classes.astype(str) | 868 classes = classes.astype(str) |
| 884 | 869 |
| 885 if resolve_rules_float != None: | 870 if resolve_rules_float != None: |
| 886 class_pat = split_class(classes, resolve_rules_float) | 871 class_pat = split_class(classes, resolve_rules_float) |
| 887 | 872 |
| 888 if args.rules_selector == 'Custom': | 873 |
| 889 if args.yes_no == 'yes': | 874 if args.custom_rules == 'true': |
| 890 try: | 875 try: |
| 891 core_map = ET.parse(args.custom_map) | 876 core_map = ET.parse(args.custom_map) |
| 892 except (ET.XMLSyntaxError, ET.XMLSchemaParseError): | 877 except (ET.XMLSyntaxError, ET.XMLSchemaParseError): |
| 893 sys.exit('Execution aborted: custom map in wrong format') | 878 sys.exit('Execution aborted: custom map in wrong format') |
| 894 elif args.yes_no == 'no': | 879 else: |
| 895 core_map = ET.parse(args.tool_dir + '/local/HMRcoreMap.svg') | |
| 896 else: | |
| 897 core_map = ET.parse(args.tool_dir+'/local/HMRcoreMap.svg') | 880 core_map = ET.parse(args.tool_dir+'/local/HMRcoreMap.svg') |
| 898 | 881 |
| 899 maps(core_map, class_pat, ids, args.pValue, args.fChange, create_svg, create_pdf, args.comparison, args.control) | 882 maps(core_map, class_pat, ids, args.pValue, args.fChange, create_svg, create_pdf, args.comparison, args.control) |
| 900 | 883 |
| 901 print('Execution succeded') | 884 print('Execution succeded') |