Mercurial > repos > bimib > marea
changeset 16:c71ac0bb12de draft
Uploaded
| author | bimib |
|---|---|
| date | Tue, 01 Oct 2019 06:05:13 -0400 |
| parents | d0e7f14b773f |
| children | 640f303d0cec |
| files | Marea/local/desktop.ini Marea/marea.py Marea/marea.xml Marea/marea_cluster.py Marea/marea_cluster.xml marea-1.0.1/local/HMRcoreMap.svg marea-1.0.1/local/HMRcore_genes.p marea-1.0.1/local/HMRcore_rules.p marea-1.0.1/local/Recon_genes.p marea-1.0.1/local/Recon_rules.p marea-1.0.1/local/desktop.ini marea-1.0.1/marea.py marea-1.0.1/marea.xml marea-1.0.1/marea_cluster.py marea-1.0.1/marea_cluster.xml marea-1.0.1/marea_macros.xml |
| diffstat | 16 files changed, 776 insertions(+), 10295 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Marea/local/desktop.ini Tue Oct 01 06:05:13 2019 -0400 @@ -0,0 +1,6 @@ +[.ShellClassInfo] +IconResource=C:\WINDOWS\System32\SHELL32.dll,4 +[ViewState] +Mode= +Vid= +FolderType=Generic
--- a/Marea/marea.py Tue Oct 01 06:03:12 2019 -0400 +++ b/Marea/marea.py Tue Oct 01 06:05:13 2019 -0400 @@ -1,4 +1,3 @@ - from __future__ import division import sys import pandas as pd @@ -6,6 +5,7 @@ import scipy.stats as st import collections import lxml.etree as ET +import shutil import pickle as pk import math import os @@ -13,7 +13,7 @@ from svglib.svglib import svg2rlg from reportlab.graphics import renderPDF -########################## argparse ########################################### +########################## argparse ########################################## def process_args(args): parser = argparse.ArgumentParser(usage = '%(prog)s [options]', @@ -71,6 +71,21 @@ type = str, choices = ['yes', 'no'], help = 'if make or not custom map') + parser.add_argument('-gs', '--generate_svg', + type = str, + default = 'true', + choices = ['true', 'false'], + help = 'generate svg map') + parser.add_argument('-gp', '--generate_pdf', + type = str, + default = 'true', + choices = ['true', 'false'], + help = 'generate pdf map') + parser.add_argument('-gr', '--generate_ras', + type = str, + default = 'true', + choices = ['true', 'false'], + help = 'generate reaction activity score') args = parser.parse_args() return args @@ -85,7 +100,7 @@ def read_dataset(data, name): try: - dataset = pd.read_csv(data, sep = '\t', header = 0) + dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python') except pd.errors.EmptyDataError: sys.exit('Execution aborted: wrong format of ' + name + '\n') if len(dataset.columns) < 2: @@ -536,7 +551,7 @@ ids = [react[i].id for i in range(len(react))] except cb.io.sbml3.CobraSBMLError: try: - data = (pd.read_csv(data, sep = '\t', dtype = str)).fillna('') + 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') @@ -641,9 +656,28 @@ ', the class has been disregarded\n') return class_pat +############################ create_ras ####################################### + +def create_ras (resolve_rules, dataset_name): + + if resolve_rules == None: + warning("Couldn't generate RAS for current dataset: " + dataset_name) + + for geni in resolve_rules.values(): + for i, valori in enumerate(geni): + if valori == None: + geni[i] = 'None' + + output_ras = pd.DataFrame.from_dict(resolve_rules) + output_to_csv = pd.DataFrame.to_csv(output_ras, sep = '\t', index = False) + + text_file = open("ras/Reaction_Activity_Score_Of_" + dataset_name + ".tsv", "w") + text_file.write(output_to_csv) + text_file.close() + ############################ map ############################################## -def maps(core_map, class_pat, ids, threshold_P_V, threshold_F_C): +def maps(core_map, class_pat, ids, threshold_P_V, threshold_F_C, create_svg, create_pdf): args = process_args(sys.argv) if (not class_pat) or (len(class_pat.keys()) < 2): sys.exit('Execution aborted: classes provided for comparisons are ' + @@ -663,52 +697,81 @@ count += 1 except (TypeError, ZeroDivisionError): count += 1 - tab = 'table_out/' + i + '_vs_' + j + '.tsv' + tab = 'result/' + i + '_vs_' + j + ' (Tabular Result).tsv' tmp_csv = pd.DataFrame.from_dict(tmp, orient = "index") tmp_csv = tmp_csv.reset_index() header = ['ids', 'P_Value', 'Average'] tmp_csv.to_csv(tab, sep = '\t', index = False, header = header) - 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 = 'map_svg/' + i + '_vs_' + j + '.svg' - with open(file_svg, 'wb') as new_map: - new_map.write(ET.tostring(core_map, encoding='UTF-8', - method='xml')) - file_pdf = 'map_pdf/' + i + '_vs_' + j + '.pdf' - renderPDF.drawToFile(svg2rlg(file_svg), file_pdf) + + if create_svg or create_pdf: + 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: + new_map.write(ET.tostring(core_map)) + + + if create_pdf: + file_pdf = 'result/' + i + '_vs_' + j + ' (PDF Map).pdf' + 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') + return None ############################ MAIN ############################################# def main(): args = process_args(sys.argv) - os.makedirs('table_out') - if args.rules_selector == 'HMRcore': - os.makedirs('map_svg') - os.makedirs('map_pdf') + + create_svg = check_bool(args.generate_svg) + create_pdf = check_bool(args.generate_pdf) + generate_ras = check_bool(args.generate_ras) + + os.makedirs('result') + + if generate_ras: + os.makedirs('ras') + + if args.rules_selector == 'HMRcore': recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb')) elif args.rules_selector == 'Recon': recon = pk.load(open(args.tool_dir + '/local/Recon_rules.p', 'rb')) elif args.rules_selector == 'Custom': ids, rules, gene_in_rule = make_recon(args.custom) + resolve_none = check_bool(args.none) + class_pat = {} + if args.option == 'datasets': num = 1 - #if len(args.names) != len(set(args.names)): - # sys.exit('Execution aborted: datasets name duplicated') for i, j in zip(args.input_datas, args.names): + name = name_dataset(j, num) dataset = read_dataset(i, name) + dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str) - type_gene = gene_type(dataset.iloc[0, 0], name) + + type_gene = gene_type(dataset.iloc[0, 0], name) + if args.rules_selector != 'Custom': genes = data_gene(dataset, type_gene, name, None) ids, rules = load_id_rules(recon.get(type_gene)) elif args.rules_selector == 'Custom': genes = data_gene(dataset, type_gene, name, gene_in_rule) + resolve_rules, err = resolve(genes, rules, ids, resolve_none, name) + + if generate_ras: + create_ras(resolve_rules, name) + + if err != None and err: warning('Warning: gene\n' + str(err) + '\nnot found in class ' + name + ', the expression level for this gene ' + @@ -738,10 +801,9 @@ 'will be considered NaN\n') if resolve_rules != None: class_pat = split_class(classes, resolve_rules) + if args.rules_selector == 'Custom': if args.yes_no == 'yes': - os.makedirs('map_svg') - os.makedirs('map_pdf') try: core_map = ET.parse(args.custom_map) except (ET.XMLSyntaxError, ET.XMLSchemaParseError): @@ -750,8 +812,11 @@ core_map = ET.parse(args.tool_dir + '/local/HMRcoreMap.svg') else: core_map = ET.parse(args.tool_dir+'/local/HMRcoreMap.svg') - maps(core_map, class_pat, ids, args.pValue, args.fChange) - warning('Execution succeeded') + + maps(core_map, class_pat, ids, args.pValue, args.fChange, create_svg, create_pdf) + + print('Execution succeded') + return None ###############################################################################
--- a/Marea/marea.xml Tue Oct 01 06:03:12 2019 -0400 +++ b/Marea/marea.xml Tue Oct 01 06:05:13 2019 -0400 @@ -1,200 +1,223 @@ -<tool id="MaREA" name="Metabolic Enrichment Analysis" version="1.0.0"> - <description>for Galaxy</description> - <macros> - <import>marea_macros.xml</import> - </macros> - <requirements> - <requirement type="package" version="0.23.0">pandas</requirement> - <requirement type="package" version="1.1.0">scipy</requirement> - <requirement type="package" version="0.10.1">cobra</requirement> - <requirement type="package" version="4.2.1">lxml</requirement> - <requirement type="package" version="0.8.1">svglib</requirement> - <requirement type="package" version="3.4.0">reportlab</requirement> - </requirements> - <command detect_errors="exit_code"> - <![CDATA[ - python $__tool_directory__/marea.py - --rules_selector $cond_rule.rules_selector - #if $cond_rule.rules_selector == 'Custom': - --custom ${cond_rule.Custom_rules} - --yes_no ${cond_rule.cond_map.yes_no} - #if $cond_rule.cond_map.yes_no == 'yes': - --custom_map $cond_rule.cond_map.Custom_map - #end if - #end if - --none $None - --pValue $pValue - --fChange $fChange - --tool_dir $__tool_directory__ - --option $cond.type_selector - --out_log $log - #if $cond.type_selector == 'datasets': - --input_datas - #for $data in $cond.input_Datasets: - ${data.input} - #end for - --names - #for $data in $cond.input_Datasets: - ${data.input_name} - #end for - #elif $cond.type_selector == 'dataset_class': - --input_data ${input_data} - --input_class ${input_class} - #end if - ]]> - </command> - - <inputs> - <conditional name="cond_rule"> - <expand macro="options"/> - <when value="HMRcore"> - </when> - <when value="Recon"> - </when> - <when value="Custom"> - <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> - <conditional name="cond_map"> - <param name="yes_no" type="select" label="Custom map? (optional)"> - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> - </when> - <when value="no"> - </when> - </conditional> - </when> - </conditional> - <conditional name="cond"> - <param name="type_selector" argument="--option" type="select" label="Input format:"> - <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option> - <option value="dataset_class">RNAseq of all samples + sample group specification</option> - </param> - <when value="datasets"> - <repeat name="input_Datasets" title="RNAseq" min="2"> - <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> - <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset" /> - </repeat> - </when> - <when value="dataset_class"> - <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> - <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> - </when> - </conditional> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> - <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" /> - <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" /> - </inputs> - - <outputs> - <data format="txt" name="log" label="Log" /> - <collection name="map_svg" type="list" label="Graphical results (.svg)"> - <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter> - <discover_datasets pattern="__name_and_ext__" directory="map_svg" /> - </collection> - <collection name="map_pdf" type="list" label="Graphical results (.pdf)"> - <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter> - <discover_datasets pattern="__name_and_ext__" directory="map_pdf" /> - </collection> - <collection name="table_out" type="list" label="Tabular results"> - <discover_datasets pattern="__name_and_ext__" directory="table_out" /> - </collection> - </outputs> - <tests> - <test> - <param name="pValue" value="0.56"/> - <output name="log" file="log.txt"/> - </test> - </tests> - <help> -<![CDATA[ - -What it does -------------- - -This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724. - -Accepted files are: - - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*"); - - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to. - -Optional files: - - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats: - - * (Cobra Toolbox and CobraPy compliant) xml of metabolic model; - * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2). - - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example. - -The tool generates: - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes; - 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes; - 3) a log file (.txt). - -RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID. - -Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2). - -To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes. - -Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA". - - -Example input -------------- - -**"Custom Rules"** option: - -Custom Rules Dastaset: - -@CUSTOM_RULES_EXEMPLE@ - -**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option: - -RNA-seq Dataset 1: - -@DATASET_EXEMPLE1@ - -RNA-seq Dataset 2: - -@DATASET_EXEMPLE2@ - -**"RNAseq of all samples + sample group specification"** option: - -RNA-seq Dataset: - -@DATASET_EXEMPLE1@ - -Class-file: - -+------------+------------+ -| Patient_ID | class | -+============+============+ -| TCGAAA3529 | MSI | -+------------+------------+ -| TCGAA62671 | MSS | -+------------+------------+ -| TCGAA62672 | MSI | -+------------+------------+ - -| - -.. class:: infomark - -**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_. - -.. class:: infomark - -**TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_. - -@REFERENCE@ - -.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724 -.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj -.. _MaREA cluster analysis: http://link del tool di cluster.org - -]]> - </help> - <expand macro="citations" /> -</tool> - +<tool id="MaREA" name="Metabolic Enrichment Analysis" version="1.0.1"> + <description>for Galaxy - 1.0.1</description> + <macros> + <import>marea_macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.23.0">pandas</requirement> + <requirement type="package" version="1.1.0">scipy</requirement> + <requirement type="package" version="0.10.1">cobra</requirement> + <requirement type="package" version="4.2.1">lxml</requirement> + <requirement type="package" version="0.8.1">svglib</requirement> + <requirement type="package" version="3.4.0">reportlab</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/marea.py + --rules_selector $cond_rule.rules_selector + #if $cond_rule.rules_selector == 'Custom': + --custom ${cond_rule.Custom_rules} + --yes_no ${cond_rule.cond_map.yes_no} + #if $cond_rule.cond_map.yes_no == 'yes': + --custom_map $cond_rule.cond_map.Custom_map + #end if + #end if + #if $advanced.choice == 'true': + --none ${advanced.None} + --pValue ${advanced.pValue} + --fChange ${advanced.fChange} + --generate_svg ${advanced.generateSvg} + --generate_pdf ${advanced.generatePdf} + --generate_ras ${advanced.generateRas} + #else + --none true + --pValue 0.05 + --fChange 1.5 + --generate_svg false + --generate_pdf true + --generate_ras false + #end if + --tool_dir $__tool_directory__ + --option $cond.type_selector + --out_log $log + + #if $cond.type_selector == 'datasets': + --input_datas + #for $data in $cond.input_Datasets: + ${data.input} + #end for + --names + #for $data in $cond.input_Datasets: + ${data.input_name} + #end for + #elif $cond.type_selector == 'dataset_class': + --input_data ${input_data} + --input_class ${input_class} + #end if + ]]> + </command> + + <inputs> + <conditional name="cond_rule"> + <expand macro="options"/> + <when value="HMRcore"> + </when> + <when value="Recon"> + </when> + <when value="Custom"> + <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> + <conditional name="cond_map"> + <param name="yes_no" type="select" label="Custom map? (optional)"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> + </when> + <when value="no"> + </when> + </conditional> + </when> + </conditional> + <conditional name="cond"> + <param name="type_selector" argument="--option" type="select" label="Input format:"> + <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option> + <option value="dataset_class">RNAseq of all samples + sample group specification</option> + </param> + <when value="datasets"> + <repeat name="input_Datasets" title="RNAseq" min="2"> + <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> + <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> + </repeat> + </when> + <when value="dataset_class"> + <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> + <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> + </when> + </conditional> + + <conditional name="advanced"> + <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> + <option value="true" selected="true">No</option> + <option value="false">Yes</option> + </param> + <when value="false"> + </when> + <when value="true"> + <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> + <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" /> + <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" /> + <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> + <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> + <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" /> + </when> + </conditional> + </inputs> + + <outputs> + <data format="txt" name="log" label="${tool.name} - Log" /> + <collection name="results" type="list" label="${tool.name} - Results"> + <discover_datasets pattern="__name_and_ext__" directory="result"/> + </collection> + <collection name="ras" type="list" label="${tool.name} - RAS" format_source="tabular"> + <filter>advanced['choice'] and advanced['generateRas']</filter> + <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/> + </collection> + </outputs> + <tests> + <test> + <param name="pValue" value="0.56"/> + <output name="log" file="log.txt"/> + </test> + </tests> + <help> +<![CDATA[ + +What it does +------------- + +This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724. + +Accepted files are: + - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*"); + - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to. + +Optional files: + - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats: + + * (Cobra Toolbox and CobraPy compliant) xml of metabolic model; + * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2). + - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example. + +The tool generates: + 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes; + 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes; + 3) a log file (.txt). + +RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID. + +Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2). + +To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes. + +Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA". + + +Example input +------------- + +**"Custom Rules"** option: + +Custom Rules Dastaset: + +@CUSTOM_RULES_EXEMPLE@ + +**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option: + +RNA-seq Dataset 1: + +@DATASET_EXEMPLE1@ + +RNA-seq Dataset 2: + +@DATASET_EXEMPLE2@ + +**"RNAseq of all samples + sample group specification"** option: + +RNA-seq Dataset: + +@DATASET_EXEMPLE1@ + +Class-file: + ++------------+------------+ +| Patient_ID | class | ++============+============+ +| TCGAAA3529 | MSI | ++------------+------------+ +| TCGAA62671 | MSS | ++------------+------------+ +| TCGAA62672 | MSI | ++------------+------------+ + +| + +.. class:: infomark + +**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_. + +.. class:: infomark + +**TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_. + +@REFERENCE@ + +.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724 +.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj +.. _MaREA cluster analysis: http://link del tool di cluster.org + +]]> + </help> + <expand macro="citations" /> +</tool> +
--- a/Marea/marea_cluster.py Tue Oct 01 06:03:12 2019 -0400 +++ b/Marea/marea_cluster.py Tue Oct 01 06:05:13 2019 -0400 @@ -1,67 +1,84 @@ -from __future__ import division -import os +# -*- coding: utf-8 -*- +""" +Created on Mon Jun 3 19:51:00 2019 + +@author: Narger +""" + import sys -import pandas as pd -import collections -import pickle as pk import argparse -from sklearn.cluster import KMeans -import matplotlib -# Force matplotlib to not use any Xwindows backend. -matplotlib.use('Agg') +import os +from sklearn.datasets import make_blobs +from sklearn.cluster import KMeans, DBSCAN, AgglomerativeClustering +from sklearn.metrics import silhouette_samples, silhouette_score, davies_bouldin_score, cluster import matplotlib.pyplot as plt +import scipy.cluster.hierarchy as shc +import matplotlib.cm as cm +import numpy as np +import pandas as pd -########################## argparse ########################################### +################################# process args ############################### def process_args(args): parser = argparse.ArgumentParser(usage = '%(prog)s [options]', description = 'process some value\'s' + ' genes to create class.') - parser.add_argument('-rs', '--rules_selector', + + parser.add_argument('-ol', '--out_log', + help = "Output log") + + parser.add_argument('-in', '--input', type = str, - default = 'HMRcore', - choices = ['HMRcore', 'Recon', 'Custom'], - help = 'chose which type of dataset you want use') - parser.add_argument('-cr', '--custom', + help = 'input dataset') + + parser.add_argument('-cy', '--cluster_type', type = str, - help='your dataset if you want custom rules') - parser.add_argument('-ch', '--cond_hier', - type = str, - default = 'no', - choices = ['no', 'yes'], - help = 'chose if you wanna hierical dendrogram') - parser.add_argument('-lk', '--k_min', + choices = ['kmeans', 'meanshift', 'dbscan', 'hierarchy'], + default = 'kmeans', + help = 'choose clustering algorythm') + + parser.add_argument('-k1', '--k_min', + type = int, + default = 2, + help = 'choose minimun cluster number to be generated') + + parser.add_argument('-k2', '--k_max', type = int, - help = 'min number of cluster') - parser.add_argument('-uk', '--k_max', - type = int, - help = 'max number of cluster') - parser.add_argument('-li', '--linkage', - type = str, - choices = ['single', 'complete', 'average'], - help='linkage hierarchical cluster') - parser.add_argument('-d', '--data', + default = 7, + help = 'choose maximum cluster number to be generated') + + parser.add_argument('-el', '--elbow', + type = str, + default = 'false', + choices = ['true', 'false'], + help = 'choose if you want to generate an elbow plot for kmeans') + + parser.add_argument('-si', '--silhouette', type = str, - required = True, - help = 'input dataset') - parser.add_argument('-n', '--none', + default = 'false', + choices = ['true', 'false'], + help = 'choose if you want silhouette plots') + + parser.add_argument('-db', '--davies', type = str, - default = 'true', - choices = ['true', 'false'], - help = 'compute Nan values') + default = 'false', + choices = ['true', 'false'], + help = 'choose if you want davies bouldin scores') + parser.add_argument('-td', '--tool_dir', type = str, required = True, help = 'your tool directory') - parser.add_argument('-na', '--name', - type = str, - help = 'name of dataset') - parser.add_argument('-de', '--dendro', - help = "Dendrogram out") - parser.add_argument('-ol', '--out_log', - help = "Output log") - parser.add_argument('-el', '--elbow', - help = "Out elbow") + + parser.add_argument('-ms', '--min_samples', + type = int, + help = 'min samples for dbscan (optional)') + + parser.add_argument('-ep', '--eps', + type = int, + help = 'eps for dbscan (optional)') + + args = parser.parse_args() return args @@ -70,548 +87,331 @@ def warning(s): args = process_args(sys.argv) with open(args.out_log, 'a') as log: - log.write(s) - -############################ dataset input #################################### + log.write(s + "\n\n") + print(s) -def read_dataset(data, name): +########################## read dataset ###################################### + +def read_dataset(dataset): try: - dataset = pd.read_csv(data, sep = '\t', header = 0) + dataset = pd.read_csv(dataset, sep = '\t', header = 0) except pd.errors.EmptyDataError: - sys.exit('Execution aborted: wrong format of '+name+'\n') + sys.exit('Execution aborted: wrong format of dataset\n') if len(dataset.columns) < 2: - sys.exit('Execution aborted: wrong format of '+name+'\n') + sys.exit('Execution aborted: wrong format of dataset\n') + return dataset + +############################ rewrite_input ################################### + +def rewrite_input(dataset): + #Riscrivo il dataset come dizionario di liste, + #non come dizionario di dizionari + + for key, val in dataset.items(): + l = [] + for i in val: + if i == 'None': + l.append(None) + else: + l.append(float(i)) + + dataset[key] = l + return dataset -############################ dataset name ##################################### - -def name_dataset(name_data, count): - if str(name_data) == 'Dataset': - return str(name_data) + '_' + str(count) - else: - return str(name_data) +############################## write to csv ################################## -############################ load id e rules ################################## - -def load_id_rules(reactions): - ids, rules = [], [] - for key, value in reactions.items(): - ids.append(key) - rules.append(value) - return (ids, rules) - -############################ check_methods #################################### - -def gene_type(l, name): - if check_hgnc(l): - return 'hugo_id' - elif check_ensembl(l): - return 'ensembl_gene_id' - elif check_symbol(l): - return 'symbol' - elif check_entrez(l): - return 'entrez_id' - else: - sys.exit('Execution aborted:\n' + - 'gene ID type in ' + name + ' not supported. Supported ID' + - 'types are: HUGO ID, Ensemble ID, HUGO symbol, Entrez ID\n') - -def check_hgnc(l): - if len(l) > 5: - if (l.upper()).startswith('HGNC:'): - return l[5:].isdigit() - else: - return False - else: - return False - -def check_ensembl(l): - if len(l) == 15: - if (l.upper()).startswith('ENS'): - return l[4:].isdigit() - else: - return False - else: - return False - -def check_symbol(l): - if len(l) > 0: - if l[0].isalpha() and l[1:].isalnum(): - return True - else: - return False - else: - return False +def write_to_csv (dataset, labels, name): + list_labels = labels + list_values = dataset -def check_entrez(l): - if len(l) > 0: - return l.isdigit() - else: - return False - -def check_bool(b): - if b == 'true': - return True - elif b == 'false': - return False + list_values = list_values.tolist() + d = {'Label' : list_labels, 'Value' : list_values} -############################ make recon ####################################### - -def check_and_doWord(l): - tmp = [] - tmp_genes = [] - count = 0 - while l: - if count >= 0: - if l[0] == '(': - count += 1 - tmp.append(l[0]) - l.pop(0) - elif l[0] == ')': - count -= 1 - tmp.append(l[0]) - l.pop(0) - elif l[0] == ' ': - l.pop(0) - else: - word = [] - while l: - if l[0] in [' ', '(', ')']: - break - else: - word.append(l[0]) - l.pop(0) - word = ''.join(word) - tmp.append(word) - if not(word in ['or', 'and']): - tmp_genes.append(word) - else: - return False - if count == 0: - return (tmp, tmp_genes) - else: - return False - -def brackets_to_list(l): - tmp = [] - while l: - if l[0] == '(': - l.pop(0) - tmp.append(resolve_brackets(l)) - else: - tmp.append(l[0]) - l.pop(0) - return tmp + df = pd.DataFrame(d, columns=['Value','Label']) -def resolve_brackets(l): - tmp = [] - while l[0] != ')': - if l[0] == '(': - l.pop(0) - tmp.append(resolve_brackets(l)) - else: - tmp.append(l[0]) - l.pop(0) - l.pop(0) - return tmp + dest = name + '.tsv' + df.to_csv(dest, sep = '\t', index = False, + header = ['Value', 'Label']) + +########################### trova il massimo in lista ######################## +def max_index (lista): + best = -1 + best_index = 0 + for i in range(len(lista)): + if lista[i] > best: + best = lista [i] + best_index = i + + return best_index + +################################ kmeans ##################################### + +def kmeans (k_min, k_max, dataset, elbow, silhouette, davies): + if not os.path.exists('clustering/kmeans_output'): + os.makedirs('clustering/kmeans_output') + + + if elbow == 'true': + elbow = True + else: + elbow = False + + if silhouette == 'true': + silhouette = True + else: + silhouette = False + + if davies == 'true': + davies = True + else: + davies = False + -def priorityAND(l): - tmp = [] - flag = True - while l: - if len(l) == 1: - if isinstance(l[0], list): - tmp.append(priorityAND(l[0])) - else: - tmp.append(l[0]) - l = l[1:] - elif l[0] == 'or': - tmp.append(l[0]) - flag = False - l = l[1:] - elif l[1] == 'or': - if isinstance(l[0], list): - tmp.append(priorityAND(l[0])) - else: - tmp.append(l[0]) - tmp.append(l[1]) - flag = False - l = l[2:] - elif l[1] == 'and': - tmpAnd = [] - if isinstance(l[0], list): - tmpAnd.append(priorityAND(l[0])) - else: - tmpAnd.append(l[0]) - tmpAnd.append(l[1]) - if isinstance(l[2], list): - tmpAnd.append(priorityAND(l[2])) - else: - tmpAnd.append(l[2]) - l = l[3:] - while l: - if l[0] == 'and': - tmpAnd.append(l[0]) - if isinstance(l[1], list): - tmpAnd.append(priorityAND(l[1])) - else: - tmpAnd.append(l[1]) - l = l[2:] - elif l[0] == 'or': - flag = False - break - if flag == True: #se ci sono solo AND nella lista - tmp.extend(tmpAnd) - elif flag == False: - tmp.append(tmpAnd) - return tmp + range_n_clusters = [i for i in range(k_min, k_max+1)] + distortions = [] + scores = [] + all_labels = [] + + for n_clusters in range_n_clusters: + clusterer = KMeans(n_clusters=n_clusters, random_state=10) + cluster_labels = clusterer.fit_predict(dataset) + + all_labels.append(cluster_labels) + silhouette_avg = silhouette_score(dataset, cluster_labels) + scores.append(silhouette_avg) + distortions.append(clusterer.fit(dataset).inertia_) + + best = max_index(scores) + k_min + + for i in range(len(all_labels)): + prefix = '' + if (i + k_min == best): + prefix = '_BEST' + + write_to_csv(dataset, all_labels[i], 'clustering/kmeans_output/kmeans_with_' + str(i + k_min) + prefix + '_clusters.tsv') + + if davies: + with np.errstate(divide='ignore', invalid='ignore'): + davies_bouldin = davies_bouldin_score(dataset, all_labels[i]) + warning("\nFor n_clusters = " + str(i + k_min) + + " The average davies bouldin score is: " + str(davies_bouldin)) + + + if silhouette: + silihouette_draw(dataset, all_labels[i], i + k_min, 'clustering/kmeans_output/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png') + + + if elbow: + elbow_plot(distortions, k_min,k_max) -def checkRule(l): - if len(l) == 1: - if isinstance(l[0], list): - if checkRule(l[0]) is False: - return False - elif len(l) > 2: - if checkRule2(l) is False: - return False - else: - return False - return True - -def checkRule2(l): - while l: - if len(l) == 1: - return False - elif isinstance(l[0], list) and l[1] in ['and', 'or']: - if checkRule(l[0]) is False: - return False - if isinstance(l[2], list): - if checkRule(l[2]) is False: - return False - l = l[3:] - elif l[1] in ['and', 'or']: - if isinstance(l[2], list): - if checkRule(l[2]) is False: - return False - l = l[3:] - elif l[0] in ['and', 'or']: - if isinstance(l[1], list): - if checkRule(l[1]) is False: - return False - l = l[2:] - else: - return False - return True - -def do_rules(rules): - split_rules = [] - err_rules = [] - tmp_gene_in_rule = [] - for i in range(len(rules)): - tmp = list(rules[i]) - if tmp: - tmp, tmp_genes = check_and_doWord(tmp) - tmp_gene_in_rule.extend(tmp_genes) - if tmp is False: - split_rules.append([]) - err_rules.append(rules[i]) - else: - tmp = brackets_to_list(tmp) - if checkRule(tmp): - split_rules.append(priorityAND(tmp)) - else: - split_rules.append([]) - err_rules.append(rules[i]) - else: - split_rules.append([]) - if err_rules: - 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.sbml3.CobraSBMLError: - try: - data = (pd.read_csv(data, sep = '\t', dtype = str)).fillna('') - if len(data.columns) < 2: - sys.exit('Execution aborted: wrong format of ' + - 'custom GPR rules\n') - if not len(data.columns) == 2: - warning('WARNING: more than 2 columns in custom GPR rules.\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 GPR rules\n') - except pd.errors.ParserError: - sys.exit('Execution aborted: wrong format of custom GPR rules\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) - -############################ resolve_methods ################################## - -def replace_gene_value(l, d): - tmp = [] - err = [] - while l: - if isinstance(l[0], list): - tmp_rules, tmp_err = replace_gene_value(l[0], d) - tmp.append(tmp_rules) - err.extend(tmp_err) - else: - value = replace_gene(l[0],d) - tmp.append(value) - if value == None: - err.append(l[0]) - l = l[1:] - return (tmp, err) - -def replace_gene(l, d): - if l =='and' or l == 'or': - return l +############################## elbow_plot #################################### + +def elbow_plot (distortions, k_min, k_max): + plt.figure(0) + plt.plot(range(k_min, k_max+1), distortions, marker = 'o') + plt.xlabel('Number of cluster') + plt.ylabel('Distortion') + s = 'clustering/kmeans_output/elbow_plot.png' + fig = plt.gcf() + fig.set_size_inches(18.5, 10.5, forward = True) + fig.savefig(s, dpi=100) + + +############################## silhouette plot ############################### +def silihouette_draw(dataset, labels, n_clusters, path): + silhouette_avg = silhouette_score(dataset, labels) + warning("For n_clusters = " + str(n_clusters) + + " The average silhouette_score is: " + str(silhouette_avg)) + + plt.close('all') + # Create a subplot with 1 row and 2 columns + fig, (ax1) = plt.subplots(1, 1) + + fig.set_size_inches(18, 7) + + # The 1st subplot is the silhouette plot + # The silhouette coefficient can range from -1, 1 but in this example all + # lie within [-0.1, 1] + ax1.set_xlim([-1, 1]) + # The (n_clusters+1)*10 is for inserting blank space between silhouette + # plots of individual clusters, to demarcate them clearly. + ax1.set_ylim([0, len(dataset) + (n_clusters + 1) * 10]) + + # Compute the silhouette scores for each sample + sample_silhouette_values = silhouette_samples(dataset, labels) + + y_lower = 10 + for i in range(n_clusters): + # Aggregate the silhouette scores for samples belonging to + # cluster i, and sort them + ith_cluster_silhouette_values = \ + sample_silhouette_values[labels == i] + + ith_cluster_silhouette_values.sort() + + size_cluster_i = ith_cluster_silhouette_values.shape[0] + y_upper = y_lower + size_cluster_i + + color = cm.nipy_spectral(float(i) / n_clusters) + ax1.fill_betweenx(np.arange(y_lower, y_upper), + 0, ith_cluster_silhouette_values, + facecolor=color, edgecolor=color, alpha=0.7) + + # Label the silhouette plots with their cluster numbers at the middle + ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i)) + + # Compute the new y_lower for next plot + y_lower = y_upper + 10 # 10 for the 0 samples + + ax1.set_title("The silhouette plot for the various clusters.") + ax1.set_xlabel("The silhouette coefficient values") + ax1.set_ylabel("Cluster label") + + # The vertical line for average silhouette score of all the values + ax1.axvline(x=silhouette_avg, color="red", linestyle="--") + + ax1.set_yticks([]) # Clear the yaxis labels / ticks + ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1]) + + + plt.suptitle(("Silhouette analysis for clustering on sample data " + "with n_clusters = " + str(n_clusters) + "\nAverage silhouette_score = " + str(silhouette_avg)), fontsize=12, fontweight='bold') + + + plt.savefig(path, bbox_inches='tight') + +######################## dbscan ############################################## + +def dbscan(dataset, eps, min_samples): + if not os.path.exists('clustering/dbscan_output'): + os.makedirs('clustering/dbscan_output') + + if eps is not None: + clusterer = DBSCAN(eps = eps, min_samples = min_samples) else: - value = d.get(l, None) - if not(value == None or isinstance(value, (int, float))): - sys.exit('Execution aborted: ' + value + ' value not valid\n') - return value - -def compute(val1, op, val2, cn): - if val1 != None and val2 != None: - if op == 'and': - return min(val1, val2) - else: - return val1 + val2 - elif op == 'and': - if cn is True: - if val1 != None: - return val1 - elif val2 != None: - return val2 - else: - return None - else: - return None - else: - if val1 != None: - return val1 - elif val2 != None: - return val2 - else: - return None - -def control(ris, l, cn): - if len(l) == 1: - if isinstance(l[0], (float, int)) or l[0] == None: - return l[0] - elif isinstance(l[0], list): - return control(None, l[0], cn) - else: - return False - elif len(l) > 2: - return control_list(ris, l, cn) - else: - return False + clusterer = DBSCAN() + + clustering = clusterer.fit(dataset) + + core_samples_mask = np.zeros_like(clustering.labels_, dtype=bool) + core_samples_mask[clustering.core_sample_indices_] = True + labels = clustering.labels_ -def control_list(ris, l, cn): - while l: - if len(l) == 1: - return False - elif (isinstance(l[0], (float, int)) or - l[0] == None) and l[1] in ['and', 'or']: - if isinstance(l[2], (float, int)) or l[2] == None: - ris = compute(l[0], l[1], l[2], cn) - elif isinstance(l[2], list): - tmp = control(None, l[2], cn) - if tmp is False: - return False - else: - ris = compute(l[0], l[1], tmp, cn) - else: - return False - l = l[3:] - elif l[0] in ['and', 'or']: - if isinstance(l[1], (float, int)) or l[1] == None: - ris = compute(ris, l[0], l[1], cn) - elif isinstance(l[1], list): - tmp = control(None,l[1], cn) - if tmp is False: - return False - else: - ris = compute(ris, l[0], tmp, cn) - else: - return False - l = l[2:] - elif isinstance(l[0], list) and l[1] in ['and', 'or']: - if isinstance(l[2], (float, int)) or l[2] == None: - tmp = control(None, l[0], cn) - if tmp is False: - return False - else: - ris = compute(tmp, l[1], l[2], cn) - elif isinstance(l[2], list): - tmp = control(None, l[0], cn) - tmp2 = control(None, l[2], cn) - if tmp is False or tmp2 is False: - return False - else: - ris = compute(tmp, l[1], tmp2, cn) - else: - return False - l = l[3:] - else: - return False - return ris + # Number of clusters in labels, ignoring noise if present. + n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0) + + silhouette_avg = silhouette_score(dataset, labels) + warning("For n_clusters =" + str(n_clusters_) + + "The average silhouette_score is :" + str(silhouette_avg)) + + ##TODO: PLOT SU DBSCAN (no centers) e HIERARCHICAL -############################ gene ############################################# + # Black removed and is used for noise instead. + unique_labels = set(labels) + colors = [plt.cm.Spectral(each) + for each in np.linspace(0, 1, len(unique_labels))] + for k, col in zip(unique_labels, colors): + if k == -1: + # Black used for noise. + col = [0, 0, 0, 1] + + class_member_mask = (labels == k) + + xy = dataset[class_member_mask & core_samples_mask] + plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col), + markeredgecolor='k', markersize=14) + + xy = dataset[class_member_mask & ~core_samples_mask] + plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col), + markeredgecolor='k', markersize=6) -def data_gene(gene, type_gene, name, gene_custom): - args = process_args(sys.argv) - for i in range(len(gene)): - tmp = gene.iloc[i, 0] - if tmp.startswith(' ') or tmp.endswith(' '): - gene.iloc[i, 0] = (tmp.lstrip()).rstrip() - gene_dup = [item for item, count in - collections.Counter(gene[gene.columns[0]]).items() if count > 1] - pat_dup = [item for item, count in - collections.Counter(list(gene.columns)).items() if count > 1] - if gene_dup: - if gene_custom == None: - if args.rules_selector == 'HMRcore': - gene_in_rule = pk.load(open(args.tool_dir + - '/local/HMRcore_genes.p', 'rb')) - elif args.rules_selector == 'Recon': - gene_in_rule = pk.load(open(args.tool_dir + - '/local/Recon_genes.p', 'rb')) - gene_in_rule = gene_in_rule.get(type_gene) - else: - gene_in_rule = gene_custom - tmp = [] - for i in gene_dup: - if gene_in_rule.get(i) == 'ok': - tmp.append(i) - if tmp: - sys.exit('Execution aborted because gene ID ' - + str(tmp) + ' in ' + name + ' is duplicated\n') - if pat_dup: - sys.exit('Execution aborted: duplicated label\n' - + str(pat_dup) + 'in ' + name + '\n') - return (gene.set_index(gene.columns[0])).to_dict() + plt.title('Estimated number of clusters: %d' % n_clusters_) + s = 'clustering/dbscan_output/dbscan_plot.png' + fig = plt.gcf() + fig.set_size_inches(18.5, 10.5, forward = True) + fig.savefig(s, dpi=100) + + + write_to_csv(dataset, labels, 'clustering/dbscan_output/dbscan_results.tsv') + +########################## hierachical ####################################### + +def hierachical_agglomerative(dataset, k_min, k_max): -############################ resolve ########################################## + if not os.path.exists('clustering/agglomerative_output'): + os.makedirs('clustering/agglomerative_output') + + plt.figure(figsize=(10, 7)) + plt.title("Customer Dendograms") + shc.dendrogram(shc.linkage(dataset, method='ward')) + fig = plt.gcf() + fig.savefig('clustering/agglomerative_output/dendogram.png', dpi=200) + + range_n_clusters = [i for i in range(k_min, k_max+1)] -def resolve(genes, rules, ids, resolve_none, name): - resolve_rules = {} - not_found = [] - flag = False - for key, value in genes.items(): - tmp_resolve = [] - for i in range(len(rules)): - tmp = rules[i] - if tmp: - tmp, err = replace_gene_value(tmp, value) - if err: - not_found.extend(err) - ris = control(None, tmp, resolve_none) - if ris is False or ris == None: - tmp_resolve.append(None) - else: - tmp_resolve.append(ris) - flag = True - else: - tmp_resolve.append(None) - resolve_rules[key] = tmp_resolve - if flag is False: - sys.exit('Execution aborted: no computable score' + - ' (due to missing gene values) for class ' - + name + ', the class has been disregarded\n') - return (resolve_rules, list(set(not_found))) - -################################# clustering ################################## + for n_clusters in range_n_clusters: + + cluster = AgglomerativeClustering(n_clusters=n_clusters, affinity='euclidean', linkage='ward') + cluster.fit_predict(dataset) + cluster_labels = cluster.labels_ + + silhouette_avg = silhouette_score(dataset, cluster_labels) + warning("For n_clusters =", n_clusters, + "The average silhouette_score is :", silhouette_avg) + + plt.clf() + plt.figure(figsize=(10, 7)) + plt.title("Agglomerative Hierarchical Clustering\nwith " + str(n_clusters) + " clusters and " + str(silhouette_avg) + " silhouette score") + plt.scatter(dataset[:,0], dataset[:,1], c = cluster_labels, cmap='rainbow') + s = 'clustering/agglomerative_output/hierachical_' + str(n_clusters) + '_clusters.png' + fig = plt.gcf() + fig.set_size_inches(10, 7, forward = True) + fig.savefig(s, dpi=200) + + write_to_csv(dataset, cluster_labels, 'clustering/agglomerative_output/agglomerative_hierarchical_with_' + str(n_clusters) + '_clusters.tsv') + + -def f_cluster(resolve_rules): - os.makedirs('cluster_out') - args = process_args(sys.argv) - k_min = args.k_min - k_max = args.k_max - if k_min > k_max: - warning('k range boundaries inverted.\n') - tmp = k_min - k_min = k_max - k_max = tmp - else: - warning('k range correct.\n') - cluster_data = pd.DataFrame.from_dict(resolve_rules, orient = 'index') - for i in cluster_data.columns: - tmp = cluster_data[i][0] - if tmp == None: - cluster_data = cluster_data.drop(columns=[i]) - distorsion = [] - for i in range(k_min, k_max+1): - tmp_kmeans = KMeans(n_clusters = i, - n_init = 100, - max_iter = 300, - random_state = 0).fit(cluster_data) - distorsion.append(tmp_kmeans.inertia_) - predict = tmp_kmeans.predict(cluster_data) - predict = [x+1 for x in predict] - classe = (pd.DataFrame(list(zip(cluster_data.index, predict)))).astype(str) - dest = 'cluster_out/K=' + str(i) + '_' + args.name+'.tsv' - classe.to_csv(dest, sep = '\t', index = False, - header = ['Patient_ID', 'Class']) - plt.figure(0) - plt.plot(range(k_min, k_max+1), distorsion, marker = 'o') - plt.xlabel('Number of cluster') - plt.ylabel('Distorsion') - plt.savefig(args.elbow, dpi = 240, format = 'pdf') - if args.cond_hier == 'yes': - import scipy.cluster.hierarchy as hier - lin = hier.linkage(cluster_data, args.linkage) - plt.figure(1) - plt.figure(figsize=(10, 5)) - hier.dendrogram(lin, leaf_font_size = 2, labels = cluster_data.index) - plt.savefig(args.dendro, dpi = 480, format = 'pdf') - return None + +############################# main ########################################### -################################# main ######################################## def main(): + if not os.path.exists('clustering'): + os.makedirs('clustering') + args = process_args(sys.argv) - if args.rules_selector == 'HMRcore': - recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb')) - elif args.rules_selector == 'Recon': - recon = pk.load(open(args.tool_dir + '/local/Recon_rules.p', 'rb')) - elif args.rules_selector == 'Custom': - ids, rules, gene_in_rule = make_recon(args.custom) - resolve_none = check_bool(args.none) - dataset = read_dataset(args.data, args.name) - dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str) - type_gene = gene_type(dataset.iloc[0, 0], args.name) - if args.rules_selector != 'Custom': - genes = data_gene(dataset, type_gene, args.name, None) - ids, rules = load_id_rules(recon.get(type_gene)) - elif args.rules_selector == 'Custom': - genes = data_gene(dataset, type_gene, args.name, gene_in_rule) - resolve_rules, err = resolve(genes, rules, ids, resolve_none, args.name) - if err: - warning('WARNING: gene\n' + str(err) + '\nnot found in class ' - + args.name + ', the expression level for this gene ' + - 'will be considered NaN\n') - f_cluster(resolve_rules) - warning('Execution succeeded') - return None - -############################################################################### + + #Data read + + X = read_dataset(args.input) + X = pd.DataFrame.to_dict(X, orient='list') + X = rewrite_input(X) + X = pd.DataFrame.from_dict(X, orient = 'index') + + for i in X.columns: + tmp = X[i][0] + if tmp == None: + X = X.drop(columns=[i]) + + X = pd.DataFrame.to_numpy(X) + + + if args.cluster_type == 'kmeans': + kmeans(args.k_min, args.k_max, X, args.elbow, args.silhouette, args.davies) + + if args.cluster_type == 'dbscan': + dbscan(X, args.eps, args.min_samples) + + if args.cluster_type == 'hierarchy': + hierachical_agglomerative(X, args.k_min, args.k_max) + +############################################################################## if __name__ == "__main__": main()
--- a/Marea/marea_cluster.xml Tue Oct 01 06:03:12 2019 -0400 +++ b/Marea/marea_cluster.xml Tue Oct 01 06:05:13 2019 -0400 @@ -1,148 +1,92 @@ -<tool id="MaREA_cluester" name="MaREA cluster analysis" version="1.0.0"> - <description>of Reaction Activity Scores</description> - <macros> - <import>marea_macros.xml</import> - </macros> - <requirements> - <requirement type="package" version="0.23.0">pandas</requirement> - <requirement type="package" version="1.1.0">scipy</requirement> - <requirement type="package" version="0.10.1">cobra</requirement> - <requirement type="package" version="0.19.1">scikit-learn</requirement> - <requirement type="package" version="2.2.2">matplotlib</requirement> - </requirements> - <command detect_errors="exit_code"> - <![CDATA[ - python $__tool_directory__/marea_cluster.py - --rules_selector $cond_rule.rules_selector - #if $cond_rule.rules_selector == 'Custom': - --custom ${cond_rule.Custom_rules} - #end if - --cond_hier $cond_hier.hier - #if $cond_hier.hier == 'yes': - --linkage ${cond_hier.linkage} - --dendro $dendrogram - #end if - --k_max $k_max - --k_min $k_min - --data $input - --name $name - --none $None - --tool_dir $__tool_directory__ - --out_log $log - --elbow $elbow - ]]> - </command> - <inputs> - <conditional name="cond_rule"> - <expand macro="options"/> - <when value="Custom"> - <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> - </when> - <when value="HMRcore"> - </when> - <when value="Recon"> - </when> - </conditional> - <param name="input" argument="--data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> - <param name="name" argument="--name" type="text" label="Output name prefix" value="dataset" /> - <param name="k_min" argument="--k_min" type="integer" size="20" value="3" min="2" max="30" label="Min number of clusters (k) to be tested (k-means)"/> - <param name="k_max" argument="--k_max" type="integer" size="20" value="3" min="2" max="30" label="Max number of clusters (k) to be tested (k-means)"/> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" help="If NO is selected, (A and NaN) is solved as (NaN)" /> - <conditional name="cond_hier"> - <param name="hier" argument="--cond_hier" type="select" label="Produce dendrogram (hierarchical clustering):"> - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param name="linkage" argument="--linkage" type="select" label="Linkage type:"> - <option value="single" selected="true">Single: minimum distance between all observations of two sets</option> - <option value="complete">Complete: maximum distance between all observations of two sets</option> - <option value="average">Average: average distance between all observations of two sets</option> - </param> - </when> - <when value="no"> - </when> - </conditional> - </inputs> - - <outputs> - <data format="txt" name="log" label="Log" /> - <data format="pdf" name="dendrogram" label="$name dendrogram"> - <filter>cond_hier['hier'] == 'yes'</filter> - </data> - <data format="pdf" name="elbow" label="$name elbow evaluation method" /> - <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max"> - <discover_datasets pattern="__name_and_ext__" directory="cluster_out" /> - </collection> - </outputs> - <tests> - <test> - <param name="k_min" value="4"/> - <output name="log" file="log.txt"/> - </test> - </tests> - <help> -<![CDATA[ - -What it does -------------- - -This tool performs cluster analysis of RNA-seq dataset(s) based of Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724. - -Accepted files are: - 1) For "Recon 2.2 rules" or "HMRcore rules" options: RNA-seq dataset. The user can specify a label of output prefix (as e.g. "K=3 *dataset*" and "K=4 *MyDataset*"); - 2) For "Custom rules" option: custom rules dataset, custom map (.svg) and RNA-seq dataset. The user can specify a label of output prefix (as e.g. "K=3 *dataset*" and "K=4 *MyDataset*"). - -Optional files: - - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats: - - * (Cobra Toolbox and CobraPy compliant) xml of metabolic model; - * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2). - - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example. - -The tool generates: - 1) Clusters n1 - n2 (n1 and n2 refer to min and max number of clusters): class-files (as many files as the chosen different number of clusters k to be tested) specifying the class/condition each sample belongs to; - 2) Log: a log file (.txt); - 3) *dataset* elbow evaluation method: diagram (.pdf) of elbow evaluation method; - 4) *dataset* dendrogram (optional): dendrogram (.pdf) if the user chooses to produce a dendrogram (hierachical clustering). - -RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID. - - -Example input -------------- - -**RNA-seq dataset**: - -@DATASET_EXEMPLE1@ - -**Custom Rules Dataset**: - -@CUSTOM_RULES_EXEMPLE@ - -**Custom Map**: - -*see the generated HMRcore .svg map for example* - - - -.. class:: infomark - -**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_. - -.. class:: warningmark - -If dendrogram it's too populated, each path and label can be not clear. - -@REFERENCE@ - -.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724 -.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj - - -]]> - </help> - <expand macro="citations" /> -</tool> - - +<tool id="MaREA_cluester" name="MaREA cluster analysis" version="1.0.1"> + <description>of Reaction Activity Scores - 1.0.1</description> + <macros> + <import>marea_macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.23.0">pandas</requirement> + <requirement type="package" version="1.1.0">scipy</requirement> + <requirement type="package" version="0.10.1">cobra</requirement> + <requirement type="package" version="0.21.3">scikit-learn</requirement> + <requirement type="package" version="2.2.2">matplotlib</requirement> + <requirement type="package" version="1.17">numpy</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/marea_cluster.py + --input $input + --tool_dir $__tool_directory__ + --out_log $log + #if $data.clust_type == 'kmeans': + --k_min ${data.k_min} + --k_max ${data.k_max} + --elbow ${data.elbow} + --silhouette ${data.silhouette} + #end if + #if $data.clust_type == 'dbscan': + #if $data.dbscan_advanced.advanced == 'true' + --eps ${data.dbscan_advanced.eps} + --min_samples ${data.dbscan_advanced.min_samples} + #end if + #end if + #if $data.clust_type == 'hierarchy': + --k_min ${data.k_min} + --k_max ${data.k_max} + #end if + ]]> + </command> + <inputs> + <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> + + <conditional name="data"> + <param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:"> + <option value="kmeans" selected="true">KMeans</option> + <option value="dbscan">DBSCAN</option> + <option value="hierarchy">Agglomerative Hierarchical</option> + </param> + <when value="kmeans"> + <param name="k_min" argument="--k_min" type="integer" min="2" max="99" value="3" label="Min number of clusters (k) to be tested" /> + <param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" /> + <param name="elbow" argument="--elbow" type="boolean" value="true" label="Draw the elbow plot from k-min to k-max"/> + <param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/> + </when> + <when value="dbscan"> + <conditional name="dbscan_advanced"> + <param name="advanced" type="boolean" value="false" label="Want to use custom params for DBSCAN? (if not optimal values will be used)"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <when value="false"></when> + <when value="true"> + <param name="eps" argument="--eps" type="float" value="0.5" label="Epsilon - The maximum distance between two samples for one to be considered as in the neighborhood of the other" /> + <param name="min_samples" argument="min_samples" type="integer" value="5" label="Min samples - The number of samples in a neighborhood for a point to be considered as a core point (this includes the point itself)"/> + + </when> + </conditional> + </when> + <when value="hierarchy"> + <param name="k_min" argument="--k_min" type="integer" min="2" max="99" value="3" label="Min number of clusters (k) to be tested" /> + <param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" /> + </when> + </conditional> + </inputs> + + <outputs> + <data format="txt" name="log" label="${tool.name} - Log" /> + <collection name="results" type="list" label="${tool.name} - Results"> + <discover_datasets pattern="__name_and_ext__" directory="clustering"/> + </collection> + </outputs> + <help> +<![CDATA[ + +What it does +------------- + + +]]> + </help> + <expand macro="citations" /> +</tool> + +
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--- a/marea-1.0.1/local/desktop.ini Tue Oct 01 06:03:12 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -[.ShellClassInfo] -IconResource=C:\WINDOWS\System32\SHELL32.dll,4 -[ViewState] -Mode= -Vid= -FolderType=Generic
--- a/marea-1.0.1/marea.py Tue Oct 01 06:03:12 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,825 +0,0 @@ -from __future__ import division -import sys -import pandas as pd -import itertools as it -import scipy.stats as st -import collections -import lxml.etree as ET -import shutil -import pickle as pk -import math -import os -import argparse -from svglib.svglib import svg2rlg -from reportlab.graphics import renderPDF - -########################## argparse ########################################## - -def process_args(args): - parser = argparse.ArgumentParser(usage = '%(prog)s [options]', - description = 'process some value\'s'+ - ' genes to create a comparison\'s map.') - parser.add_argument('-rs', '--rules_selector', - type = str, - default = 'HMRcore', - choices = ['HMRcore', 'Recon', 'Custom'], - help = 'chose which type of dataset you want use') - parser.add_argument('-cr', '--custom', - type = str, - help='your dataset if you want custom rules') - parser.add_argument('-na', '--names', - type = str, - nargs = '+', - help = 'input names') - parser.add_argument('-n', '--none', - type = str, - default = 'true', - choices = ['true', 'false'], - help = 'compute Nan values') - parser.add_argument('-pv' ,'--pValue', - type = float, - default = 0.05, - help = 'P-Value threshold (default: %(default)s)') - parser.add_argument('-fc', '--fChange', - type = float, - default = 1.5, - help = 'Fold-Change threshold (default: %(default)s)') - parser.add_argument('-td', '--tool_dir', - type = str, - required = True, - help = 'your tool directory') - parser.add_argument('-op', '--option', - type = str, - choices = ['datasets', 'dataset_class'], - help='dataset or dataset and class') - parser.add_argument('-ol', '--out_log', - help = "Output log") - parser.add_argument('-ids', '--input_datas', - type = str, - nargs = '+', - help = 'input datasets') - parser.add_argument('-id', '--input_data', - type = str, - help = 'input dataset') - parser.add_argument('-ic', '--input_class', - type = str, - help = 'sample group specification') - parser.add_argument('-cm', '--custom_map', - type = str, - help = 'custom map') - parser.add_argument('-yn', '--yes_no', - type = str, - choices = ['yes', 'no'], - help = 'if make or not custom map') - parser.add_argument('-gs', '--generate_svg', - type = str, - default = 'true', - choices = ['true', 'false'], - help = 'generate svg map') - parser.add_argument('-gp', '--generate_pdf', - type = str, - default = 'true', - choices = ['true', 'false'], - help = 'generate pdf map') - parser.add_argument('-gr', '--generate_ras', - type = str, - default = 'true', - choices = ['true', 'false'], - help = 'generate reaction activity score') - args = parser.parse_args() - return args - -########################### warning ########################################### - -def warning(s): - args = process_args(sys.argv) - with open(args.out_log, 'a') as log: - log.write(s) - -############################ dataset input #################################### - -def read_dataset(data, name): - try: - dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python') - except pd.errors.EmptyDataError: - sys.exit('Execution aborted: wrong format of ' + name + '\n') - if len(dataset.columns) < 2: - sys.exit('Execution aborted: wrong format of ' + name + '\n') - return dataset - -############################ dataset name ##################################### - -def name_dataset(name_data, count): - if str(name_data) == 'Dataset': - return str(name_data) + '_' + str(count) - else: - return str(name_data) - -############################ load id e rules ################################## - -def load_id_rules(reactions): - ids, rules = [], [] - for key, value in reactions.items(): - ids.append(key) - rules.append(value) - return (ids, rules) - -############################ check_methods #################################### - -def gene_type(l, name): - if check_hgnc(l): - return 'hugo_id' - elif check_ensembl(l): - return 'ensembl_gene_id' - elif check_symbol(l): - return 'symbol' - elif check_entrez(l): - return 'entrez_id' - else: - sys.exit('Execution aborted:\n' + - 'gene ID type in ' + name + ' not supported. Supported ID'+ - 'types are: HUGO ID, Ensemble ID, HUGO symbol, Entrez ID\n') - -def check_hgnc(l): - if len(l) > 5: - if (l.upper()).startswith('HGNC:'): - return l[5:].isdigit() - else: - return False - else: - return False - -def check_ensembl(l): - if len(l) == 15: - if (l.upper()).startswith('ENS'): - return l[4:].isdigit() - else: - return False - else: - return False - -def check_symbol(l): - if len(l) > 0: - if l[0].isalpha() and l[1:].isalnum(): - return True - else: - return False - else: - return False - -def check_entrez(l): - if len(l) > 0: - return l.isdigit() - else: - return False - -def check_bool(b): - if b == 'true': - return True - elif b == 'false': - return False - -############################ resolve_methods ################################## - -def replace_gene_value(l, d): - tmp = [] - err = [] - while l: - if isinstance(l[0], list): - tmp_rules, tmp_err = replace_gene_value(l[0], d) - tmp.append(tmp_rules) - err.extend(tmp_err) - else: - value = replace_gene(l[0], d) - tmp.append(value) - if value == None: - err.append(l[0]) - l = l[1:] - return (tmp, err) - -def replace_gene(l, d): - if l =='and' or l == 'or': - return l - else: - value = d.get(l, None) - if not(value == None or isinstance(value, (int, float))): - sys.exit('Execution aborted: ' + value + ' value not valid\n') - return value - -def computes(val1, op, val2, cn): - if val1 != None and val2 != None: - if op == 'and': - return min(val1, val2) - else: - return val1 + val2 - elif op == 'and': - if cn is True: - if val1 != None: - return val1 - elif val2 != None: - return val2 - else: - return None - else: - return None - else: - if val1 != None: - return val1 - elif val2 != None: - return val2 - else: - return None - -def control(ris, l, cn): - if len(l) == 1: - if isinstance(l[0], (float, int)) or l[0] == None: - return l[0] - elif isinstance(l[0], list): - return control(None, l[0], cn) - else: - return False - elif len(l) > 2: - return control_list(ris, l, cn) - else: - return False - -def control_list(ris, l, cn): - while l: - if len(l) == 1: - return False - elif (isinstance(l[0], (float, int)) or - l[0] == None) and l[1] in ['and', 'or']: - if isinstance(l[2], (float, int)) or l[2] == None: - ris = computes(l[0], l[1], l[2], cn) - elif isinstance(l[2], list): - tmp = control(None, l[2], cn) - if tmp is False: - return False - else: - ris = computes(l[0], l[1], tmp, cn) - else: - return False - l = l[3:] - elif l[0] in ['and', 'or']: - if isinstance(l[1], (float, int)) or l[1] == None: - ris = computes(ris, l[0], l[1], cn) - elif isinstance(l[1], list): - tmp = control(None,l[1], cn) - if tmp is False: - return False - else: - ris = computes(ris, l[0], tmp, cn) - else: - return False - l = l[2:] - elif isinstance(l[0], list) and l[1] in ['and', 'or']: - if isinstance(l[2], (float, int)) or l[2] == None: - tmp = control(None, l[0], cn) - if tmp is False: - return False - else: - ris = computes(tmp, l[1], l[2], cn) - elif isinstance(l[2], list): - tmp = control(None, l[0], cn) - tmp2 = control(None, l[2], cn) - if tmp is False or tmp2 is False: - return False - else: - ris = computes(tmp, l[1], tmp2, cn) - else: - return False - l = l[3:] - else: - return False - return ris - -############################ map_methods ###################################### - -def fold_change(avg1, avg2): - if avg1 == 0 and avg2 == 0: - return 0 - elif avg1 == 0: - return '-INF' - elif avg2 == 0: - return 'INF' - else: - return math.log(avg1 / avg2, 2) - -def fix_style(l, col, width, dash): - tmp = l.split(';') - flag_col = False - flag_width = False - flag_dash = False - for i in range(len(tmp)): - if tmp[i].startswith('stroke:'): - tmp[i] = 'stroke:' + col - flag_col = True - if tmp[i].startswith('stroke-width:'): - tmp[i] = 'stroke-width:' + width - flag_width = True - if tmp[i].startswith('stroke-dasharray:'): - tmp[i] = 'stroke-dasharray:' + dash - flag_dash = True - if not flag_col: - tmp.append('stroke:' + col) - if not flag_width: - tmp.append('stroke-width:' + width) - if not flag_dash: - tmp.append('stroke-dasharray:' + dash) - return ';'.join(tmp) - -def fix_map(d, core_map, threshold_P_V, threshold_F_C, max_F_C): - maxT = 12 - minT = 2 - grey = '#BEBEBE' - blue = '#0000FF' - red = '#E41A1C' - for el in core_map.iter(): - el_id = str(el.get('id')) - if el_id.startswith('R_'): - tmp = d.get(el_id[2:]) - if tmp != None: - p_val = tmp[0] - f_c = tmp[1] - if p_val < threshold_P_V: - if not isinstance(f_c, str): - if abs(f_c) < math.log(threshold_F_C, 2): - col = grey - width = str(minT) - else: - if f_c < 0: - col = blue - elif f_c > 0: - col = red - width = str(max((abs(f_c) * maxT) / max_F_C, minT)) - else: - if f_c == '-INF': - col = blue - elif f_c == 'INF': - col = red - width = str(maxT) - dash = 'none' - else: - dash = '5,5' - col = grey - width = str(minT) - el.set('style', fix_style(el.get('style'), col, width, dash)) - return core_map - -############################ make recon ####################################### - -def check_and_doWord(l): - tmp = [] - tmp_genes = [] - count = 0 - while l: - if count >= 0: - if l[0] == '(': - count += 1 - tmp.append(l[0]) - l.pop(0) - elif l[0] == ')': - count -= 1 - tmp.append(l[0]) - l.pop(0) - elif l[0] == ' ': - l.pop(0) - else: - word = [] - while l: - if l[0] in [' ', '(', ')']: - break - else: - word.append(l[0]) - l.pop(0) - word = ''.join(word) - tmp.append(word) - if not(word in ['or', 'and']): - tmp_genes.append(word) - else: - return False - if count == 0: - return (tmp, tmp_genes) - else: - return False - -def brackets_to_list(l): - tmp = [] - while l: - if l[0] == '(': - l.pop(0) - tmp.append(resolve_brackets(l)) - else: - tmp.append(l[0]) - l.pop(0) - return tmp - -def resolve_brackets(l): - tmp = [] - while l[0] != ')': - if l[0] == '(': - l.pop(0) - tmp.append(resolve_brackets(l)) - else: - tmp.append(l[0]) - l.pop(0) - l.pop(0) - return tmp - -def priorityAND(l): - tmp = [] - flag = True - while l: - if len(l) == 1: - if isinstance(l[0], list): - tmp.append(priorityAND(l[0])) - else: - tmp.append(l[0]) - l = l[1:] - elif l[0] == 'or': - tmp.append(l[0]) - flag = False - l = l[1:] - elif l[1] == 'or': - if isinstance(l[0], list): - tmp.append(priorityAND(l[0])) - else: - tmp.append(l[0]) - tmp.append(l[1]) - flag = False - l = l[2:] - elif l[1] == 'and': - tmpAnd = [] - if isinstance(l[0], list): - tmpAnd.append(priorityAND(l[0])) - else: - tmpAnd.append(l[0]) - tmpAnd.append(l[1]) - if isinstance(l[2], list): - tmpAnd.append(priorityAND(l[2])) - else: - tmpAnd.append(l[2]) - l = l[3:] - while l: - if l[0] == 'and': - tmpAnd.append(l[0]) - if isinstance(l[1], list): - tmpAnd.append(priorityAND(l[1])) - else: - tmpAnd.append(l[1]) - l = l[2:] - elif l[0] == 'or': - flag = False - break - if flag == True: #when there are only AND in list - tmp.extend(tmpAnd) - elif flag == False: - tmp.append(tmpAnd) - return tmp - -def checkRule(l): - if len(l) == 1: - if isinstance(l[0], list): - if checkRule(l[0]) is False: - return False - elif len(l) > 2: - if checkRule2(l) is False: - return False - else: - return False - return True - -def checkRule2(l): - while l: - if len(l) == 1: - return False - elif isinstance(l[0], list) and l[1] in ['and', 'or']: - if checkRule(l[0]) is False: - return False - if isinstance(l[2], list): - if checkRule(l[2]) is False: - return False - l = l[3:] - elif l[1] in ['and', 'or']: - if isinstance(l[2], list): - if checkRule(l[2]) is False: - return False - l = l[3:] - elif l[0] in ['and', 'or']: - if isinstance(l[1], list): - if checkRule(l[1]) is False: - return False - l = l[2:] - else: - return False - return True - -def do_rules(rules): - split_rules = [] - err_rules = [] - tmp_gene_in_rule = [] - for i in range(len(rules)): - tmp = list(rules[i]) - if tmp: - tmp, tmp_genes = check_and_doWord(tmp) - tmp_gene_in_rule.extend(tmp_genes) - if tmp is False: - split_rules.append([]) - err_rules.append(rules[i]) - else: - tmp = brackets_to_list(tmp) - if checkRule(tmp): - split_rules.append(priorityAND(tmp)) - else: - split_rules.append([]) - err_rules.append(rules[i]) - else: - split_rules.append([]) - if err_rules: - 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.sbml3.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 ############################################# - -def data_gene(gene, type_gene, name, gene_custom): - args = process_args(sys.argv) - for i in range(len(gene)): - tmp = gene.iloc[i, 0] - if tmp.startswith(' ') or tmp.endswith(' '): - gene.iloc[i, 0] = (tmp.lstrip()).rstrip() - gene_dup = [item for item, count in - collections.Counter(gene[gene.columns[0]]).items() if count > 1] - pat_dup = [item for item, count in - collections.Counter(list(gene.columns)).items() if count > 1] - if gene_dup: - if gene_custom == None: - if args.rules_selector == 'HMRcore': - gene_in_rule = pk.load(open(args.tool_dir + - '/local/HMRcore_genes.p', 'rb')) - elif args.rules_selector == 'Recon': - gene_in_rule = pk.load(open(args.tool_dir + - '/local/Recon_genes.p', 'rb')) - gene_in_rule = gene_in_rule.get(type_gene) - else: - gene_in_rule = gene_custom - tmp = [] - for i in gene_dup: - if gene_in_rule.get(i) == 'ok': - tmp.append(i) - if tmp: - sys.exit('Execution aborted because gene ID ' - +str(tmp)+' in '+name+' is duplicated\n') - if pat_dup: - warning('Warning: duplicated label\n' + str(pat_dup) + 'in ' + name + - '\n') - return (gene.set_index(gene.columns[0])).to_dict() - -############################ resolve ########################################## - -def resolve(genes, rules, ids, resolve_none, name): - resolve_rules = {} - not_found = [] - flag = False - for key, value in genes.items(): - tmp_resolve = [] - for i in range(len(rules)): - tmp = rules[i] - if tmp: - tmp, err = replace_gene_value(tmp, value) - if err: - not_found.extend(err) - ris = control(None, tmp, resolve_none) - if ris is False or ris == None: - tmp_resolve.append(None) - else: - tmp_resolve.append(ris) - flag = True - else: - tmp_resolve.append(None) - resolve_rules[key] = tmp_resolve - if flag is False: - warning('Warning: no computable score (due to missing gene values)' + - 'for class ' + name + ', the class has been disregarded\n') - return (None, None) - return (resolve_rules, list(set(not_found))) - -############################ split class ###################################### - -def split_class(classes, resolve_rules): - class_pat = {} - for i in range(len(classes)): - classe = classes.iloc[i, 1] - if not pd.isnull(classe): - l = [] - for j in range(i, len(classes)): - if classes.iloc[j, 1] == classe: - pat_id = classes.iloc[j, 0] - tmp = resolve_rules.get(pat_id, None) - if tmp != None: - l.append(tmp) - classes.iloc[j, 1] = None - if l: - class_pat[classe] = list(map(list, zip(*l))) - else: - warning('Warning: no sample found in class ' + classe + - ', the class has been disregarded\n') - return class_pat - -############################ create_ras ####################################### - -def create_ras (resolve_rules, dataset_name): - - if resolve_rules == None: - warning("Couldn't generate RAS for current dataset: " + dataset_name) - - for geni in resolve_rules.values(): - for i, valori in enumerate(geni): - if valori == None: - geni[i] = 'None' - - output_ras = pd.DataFrame.from_dict(resolve_rules) - output_to_csv = pd.DataFrame.to_csv(output_ras, sep = '\t', index = False) - - text_file = open("ras/Reaction_Activity_Score_Of_" + dataset_name + ".tsv", "w") - text_file.write(output_to_csv) - text_file.close() - -############################ map ############################################## - -def maps(core_map, class_pat, ids, threshold_P_V, threshold_F_C, create_svg, create_pdf): - args = process_args(sys.argv) - if (not class_pat) or (len(class_pat.keys()) < 2): - sys.exit('Execution aborted: classes provided for comparisons are ' + - 'less than two\n') - for i, j in it.combinations(class_pat.keys(), 2): - tmp = {} - count = 0 - max_F_C = 0 - for l1, l2 in zip(class_pat.get(i), class_pat.get(j)): - try: - stat_D, p_value = st.ks_2samp(l1, l2) - avg = fold_change(sum(l1) / len(l1), sum(l2) / len(l2)) - if not isinstance(avg, str): - if max_F_C < abs(avg): - max_F_C = abs(avg) - tmp[ids[count]] = [float(p_value), avg] - count += 1 - except (TypeError, ZeroDivisionError): - count += 1 - tab = 'result/' + i + '_vs_' + j + ' (Tabular Result).tsv' - tmp_csv = pd.DataFrame.from_dict(tmp, orient = "index") - tmp_csv = tmp_csv.reset_index() - header = ['ids', 'P_Value', 'Average'] - tmp_csv.to_csv(tab, sep = '\t', index = False, header = header) - - if create_svg or create_pdf: - 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: - new_map.write(ET.tostring(core_map)) - - - if create_pdf: - file_pdf = 'result/' + i + '_vs_' + j + ' (PDF Map).pdf' - 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') - - return None - -############################ MAIN ############################################# - -def main(): - args = process_args(sys.argv) - - create_svg = check_bool(args.generate_svg) - create_pdf = check_bool(args.generate_pdf) - generate_ras = check_bool(args.generate_ras) - - os.makedirs('result') - - if generate_ras: - os.makedirs('ras') - - if args.rules_selector == 'HMRcore': - recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb')) - elif args.rules_selector == 'Recon': - recon = pk.load(open(args.tool_dir + '/local/Recon_rules.p', 'rb')) - elif args.rules_selector == 'Custom': - ids, rules, gene_in_rule = make_recon(args.custom) - - resolve_none = check_bool(args.none) - - class_pat = {} - - if args.option == 'datasets': - num = 1 - for i, j in zip(args.input_datas, args.names): - - name = name_dataset(j, num) - dataset = read_dataset(i, name) - - dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str) - - type_gene = gene_type(dataset.iloc[0, 0], name) - - if args.rules_selector != 'Custom': - genes = data_gene(dataset, type_gene, name, None) - ids, rules = load_id_rules(recon.get(type_gene)) - elif args.rules_selector == 'Custom': - genes = data_gene(dataset, type_gene, name, gene_in_rule) - - resolve_rules, err = resolve(genes, rules, ids, resolve_none, name) - - if generate_ras: - create_ras(resolve_rules, name) - - - if err != None and err: - warning('Warning: gene\n' + str(err) + '\nnot found in class ' - + name + ', the expression level for this gene ' + - 'will be considered NaN\n') - if resolve_rules != None: - class_pat[name] = list(map(list, zip(*resolve_rules.values()))) - num += 1 - elif args.option == 'dataset_class': - name = 'RNAseq' - dataset = read_dataset(args.input_data, name) - dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str) - type_gene = gene_type(dataset.iloc[0, 0], name) - classes = read_dataset(args.input_class, 'class') - if not len(classes.columns) == 2: - warning('Warning: more than 2 columns in class file. Extra' + - 'columns have been disregarded\n') - classes = classes.astype(str) - if args.rules_selector != 'Custom': - genes = data_gene(dataset, type_gene, name, None) - ids, rules = load_id_rules(recon.get(type_gene)) - elif args.rules_selector == 'Custom': - genes = data_gene(dataset, type_gene, name, gene_in_rule) - resolve_rules, err = resolve(genes, rules, ids, resolve_none, name) - if err != None and err: - warning('Warning: gene\n'+str(err)+'\nnot found in class ' - + name + ', the expression level for this gene ' + - 'will be considered NaN\n') - if resolve_rules != None: - class_pat = split_class(classes, resolve_rules) - - if args.rules_selector == 'Custom': - if args.yes_no == 'yes': - try: - core_map = ET.parse(args.custom_map) - except (ET.XMLSyntaxError, ET.XMLSchemaParseError): - sys.exit('Execution aborted: custom map in wrong format') - elif args.yes_no == 'no': - core_map = ET.parse(args.tool_dir + '/local/HMRcoreMap.svg') - else: - core_map = ET.parse(args.tool_dir+'/local/HMRcoreMap.svg') - - maps(core_map, class_pat, ids, args.pValue, args.fChange, create_svg, create_pdf) - - print('Execution succeded') - - return None - -############################################################################### - -if __name__ == "__main__": - main()
--- a/marea-1.0.1/marea.xml Tue Oct 01 06:03:12 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,223 +0,0 @@ -<tool id="MaREA" name="Metabolic Enrichment Analysis" version="1.0.1"> - <description>for Galaxy - 1.0.1</description> - <macros> - <import>marea_macros.xml</import> - </macros> - <requirements> - <requirement type="package" version="0.23.0">pandas</requirement> - <requirement type="package" version="1.1.0">scipy</requirement> - <requirement type="package" version="0.10.1">cobra</requirement> - <requirement type="package" version="4.2.1">lxml</requirement> - <requirement type="package" version="0.8.1">svglib</requirement> - <requirement type="package" version="3.4.0">reportlab</requirement> - </requirements> - <command detect_errors="exit_code"> - <![CDATA[ - python $__tool_directory__/marea.py - --rules_selector $cond_rule.rules_selector - #if $cond_rule.rules_selector == 'Custom': - --custom ${cond_rule.Custom_rules} - --yes_no ${cond_rule.cond_map.yes_no} - #if $cond_rule.cond_map.yes_no == 'yes': - --custom_map $cond_rule.cond_map.Custom_map - #end if - #end if - #if $advanced.choice == 'true': - --none ${advanced.None} - --pValue ${advanced.pValue} - --fChange ${advanced.fChange} - --generate_svg ${advanced.generateSvg} - --generate_pdf ${advanced.generatePdf} - --generate_ras ${advanced.generateRas} - #else - --none true - --pValue 0.05 - --fChange 1.5 - --generate_svg false - --generate_pdf true - --generate_ras false - #end if - --tool_dir $__tool_directory__ - --option $cond.type_selector - --out_log $log - - #if $cond.type_selector == 'datasets': - --input_datas - #for $data in $cond.input_Datasets: - ${data.input} - #end for - --names - #for $data in $cond.input_Datasets: - ${data.input_name} - #end for - #elif $cond.type_selector == 'dataset_class': - --input_data ${input_data} - --input_class ${input_class} - #end if - ]]> - </command> - - <inputs> - <conditional name="cond_rule"> - <expand macro="options"/> - <when value="HMRcore"> - </when> - <when value="Recon"> - </when> - <when value="Custom"> - <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> - <conditional name="cond_map"> - <param name="yes_no" type="select" label="Custom map? (optional)"> - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> - </when> - <when value="no"> - </when> - </conditional> - </when> - </conditional> - <conditional name="cond"> - <param name="type_selector" argument="--option" type="select" label="Input format:"> - <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option> - <option value="dataset_class">RNAseq of all samples + sample group specification</option> - </param> - <when value="datasets"> - <repeat name="input_Datasets" title="RNAseq" min="2"> - <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> - <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> - </repeat> - </when> - <when value="dataset_class"> - <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> - <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> - </when> - </conditional> - - <conditional name="advanced"> - <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> - <option value="true" selected="true">No</option> - <option value="false">Yes</option> - </param> - <when value="false"> - </when> - <when value="true"> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> - <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" /> - <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" /> - <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> - <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> - <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" /> - </when> - </conditional> - </inputs> - - <outputs> - <data format="txt" name="log" label="${tool.name} - Log" /> - <collection name="results" type="list" label="${tool.name} - Results"> - <discover_datasets pattern="__name_and_ext__" directory="result"/> - </collection> - <collection name="ras" type="list" label="${tool.name} - RAS" format_source="tabular"> - <filter>advanced['choice'] and advanced['generateRas']</filter> - <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/> - </collection> - </outputs> - <tests> - <test> - <param name="pValue" value="0.56"/> - <output name="log" file="log.txt"/> - </test> - </tests> - <help> -<![CDATA[ - -What it does -------------- - -This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724. - -Accepted files are: - - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*"); - - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to. - -Optional files: - - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats: - - * (Cobra Toolbox and CobraPy compliant) xml of metabolic model; - * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2). - - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example. - -The tool generates: - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes; - 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes; - 3) a log file (.txt). - -RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID. - -Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2). - -To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes. - -Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA". - - -Example input -------------- - -**"Custom Rules"** option: - -Custom Rules Dastaset: - -@CUSTOM_RULES_EXEMPLE@ - -**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option: - -RNA-seq Dataset 1: - -@DATASET_EXEMPLE1@ - -RNA-seq Dataset 2: - -@DATASET_EXEMPLE2@ - -**"RNAseq of all samples + sample group specification"** option: - -RNA-seq Dataset: - -@DATASET_EXEMPLE1@ - -Class-file: - -+------------+------------+ -| Patient_ID | class | -+============+============+ -| TCGAAA3529 | MSI | -+------------+------------+ -| TCGAA62671 | MSS | -+------------+------------+ -| TCGAA62672 | MSI | -+------------+------------+ - -| - -.. class:: infomark - -**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_. - -.. class:: infomark - -**TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_. - -@REFERENCE@ - -.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724 -.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj -.. _MaREA cluster analysis: http://link del tool di cluster.org - -]]> - </help> - <expand macro="citations" /> -</tool> -
--- a/marea-1.0.1/marea_cluster.py Tue Oct 01 06:03:12 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,417 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Mon Jun 3 19:51:00 2019 - -@author: Narger -""" - -import sys -import argparse -import os -from sklearn.datasets import make_blobs -from sklearn.cluster import KMeans, DBSCAN, AgglomerativeClustering -from sklearn.metrics import silhouette_samples, silhouette_score, davies_bouldin_score, cluster -import matplotlib.pyplot as plt -import scipy.cluster.hierarchy as shc -import matplotlib.cm as cm -import numpy as np -import pandas as pd - -################################# process args ############################### - -def process_args(args): - parser = argparse.ArgumentParser(usage = '%(prog)s [options]', - description = 'process some value\'s' + - ' genes to create class.') - - parser.add_argument('-ol', '--out_log', - help = "Output log") - - parser.add_argument('-in', '--input', - type = str, - help = 'input dataset') - - parser.add_argument('-cy', '--cluster_type', - type = str, - choices = ['kmeans', 'meanshift', 'dbscan', 'hierarchy'], - default = 'kmeans', - help = 'choose clustering algorythm') - - parser.add_argument('-k1', '--k_min', - type = int, - default = 2, - help = 'choose minimun cluster number to be generated') - - parser.add_argument('-k2', '--k_max', - type = int, - default = 7, - help = 'choose maximum cluster number to be generated') - - parser.add_argument('-el', '--elbow', - type = str, - default = 'false', - choices = ['true', 'false'], - help = 'choose if you want to generate an elbow plot for kmeans') - - parser.add_argument('-si', '--silhouette', - type = str, - default = 'false', - choices = ['true', 'false'], - help = 'choose if you want silhouette plots') - - parser.add_argument('-db', '--davies', - type = str, - default = 'false', - choices = ['true', 'false'], - help = 'choose if you want davies bouldin scores') - - parser.add_argument('-td', '--tool_dir', - type = str, - required = True, - help = 'your tool directory') - - parser.add_argument('-ms', '--min_samples', - type = int, - help = 'min samples for dbscan (optional)') - - parser.add_argument('-ep', '--eps', - type = int, - help = 'eps for dbscan (optional)') - - - args = parser.parse_args() - return args - -########################### warning ########################################### - -def warning(s): - args = process_args(sys.argv) - with open(args.out_log, 'a') as log: - log.write(s + "\n\n") - print(s) - -########################## read dataset ###################################### - -def read_dataset(dataset): - try: - dataset = pd.read_csv(dataset, sep = '\t', header = 0) - except pd.errors.EmptyDataError: - sys.exit('Execution aborted: wrong format of dataset\n') - if len(dataset.columns) < 2: - sys.exit('Execution aborted: wrong format of dataset\n') - return dataset - -############################ rewrite_input ################################### - -def rewrite_input(dataset): - #Riscrivo il dataset come dizionario di liste, - #non come dizionario di dizionari - - for key, val in dataset.items(): - l = [] - for i in val: - if i == 'None': - l.append(None) - else: - l.append(float(i)) - - dataset[key] = l - - return dataset - -############################## write to csv ################################## - -def write_to_csv (dataset, labels, name): - list_labels = labels - list_values = dataset - - list_values = list_values.tolist() - d = {'Label' : list_labels, 'Value' : list_values} - - df = pd.DataFrame(d, columns=['Value','Label']) - - dest = name + '.tsv' - df.to_csv(dest, sep = '\t', index = False, - header = ['Value', 'Label']) - -########################### trova il massimo in lista ######################## -def max_index (lista): - best = -1 - best_index = 0 - for i in range(len(lista)): - if lista[i] > best: - best = lista [i] - best_index = i - - return best_index - -################################ kmeans ##################################### - -def kmeans (k_min, k_max, dataset, elbow, silhouette, davies): - if not os.path.exists('clustering/kmeans_output'): - os.makedirs('clustering/kmeans_output') - - - if elbow == 'true': - elbow = True - else: - elbow = False - - if silhouette == 'true': - silhouette = True - else: - silhouette = False - - if davies == 'true': - davies = True - else: - davies = False - - - range_n_clusters = [i for i in range(k_min, k_max+1)] - distortions = [] - scores = [] - all_labels = [] - - for n_clusters in range_n_clusters: - clusterer = KMeans(n_clusters=n_clusters, random_state=10) - cluster_labels = clusterer.fit_predict(dataset) - - all_labels.append(cluster_labels) - silhouette_avg = silhouette_score(dataset, cluster_labels) - scores.append(silhouette_avg) - distortions.append(clusterer.fit(dataset).inertia_) - - best = max_index(scores) + k_min - - for i in range(len(all_labels)): - prefix = '' - if (i + k_min == best): - prefix = '_BEST' - - write_to_csv(dataset, all_labels[i], 'clustering/kmeans_output/kmeans_with_' + str(i + k_min) + prefix + '_clusters.tsv') - - if davies: - with np.errstate(divide='ignore', invalid='ignore'): - davies_bouldin = davies_bouldin_score(dataset, all_labels[i]) - warning("\nFor n_clusters = " + str(i + k_min) + - " The average davies bouldin score is: " + str(davies_bouldin)) - - - if silhouette: - silihouette_draw(dataset, all_labels[i], i + k_min, 'clustering/kmeans_output/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png') - - - if elbow: - elbow_plot(distortions, k_min,k_max) - - - - - -############################## elbow_plot #################################### - -def elbow_plot (distortions, k_min, k_max): - plt.figure(0) - plt.plot(range(k_min, k_max+1), distortions, marker = 'o') - plt.xlabel('Number of cluster') - plt.ylabel('Distortion') - s = 'clustering/kmeans_output/elbow_plot.png' - fig = plt.gcf() - fig.set_size_inches(18.5, 10.5, forward = True) - fig.savefig(s, dpi=100) - - -############################## silhouette plot ############################### -def silihouette_draw(dataset, labels, n_clusters, path): - silhouette_avg = silhouette_score(dataset, labels) - warning("For n_clusters = " + str(n_clusters) + - " The average silhouette_score is: " + str(silhouette_avg)) - - plt.close('all') - # Create a subplot with 1 row and 2 columns - fig, (ax1) = plt.subplots(1, 1) - - fig.set_size_inches(18, 7) - - # The 1st subplot is the silhouette plot - # The silhouette coefficient can range from -1, 1 but in this example all - # lie within [-0.1, 1] - ax1.set_xlim([-1, 1]) - # The (n_clusters+1)*10 is for inserting blank space between silhouette - # plots of individual clusters, to demarcate them clearly. - ax1.set_ylim([0, len(dataset) + (n_clusters + 1) * 10]) - - # Compute the silhouette scores for each sample - sample_silhouette_values = silhouette_samples(dataset, labels) - - y_lower = 10 - for i in range(n_clusters): - # Aggregate the silhouette scores for samples belonging to - # cluster i, and sort them - ith_cluster_silhouette_values = \ - sample_silhouette_values[labels == i] - - ith_cluster_silhouette_values.sort() - - size_cluster_i = ith_cluster_silhouette_values.shape[0] - y_upper = y_lower + size_cluster_i - - color = cm.nipy_spectral(float(i) / n_clusters) - ax1.fill_betweenx(np.arange(y_lower, y_upper), - 0, ith_cluster_silhouette_values, - facecolor=color, edgecolor=color, alpha=0.7) - - # Label the silhouette plots with their cluster numbers at the middle - ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i)) - - # Compute the new y_lower for next plot - y_lower = y_upper + 10 # 10 for the 0 samples - - ax1.set_title("The silhouette plot for the various clusters.") - ax1.set_xlabel("The silhouette coefficient values") - ax1.set_ylabel("Cluster label") - - # The vertical line for average silhouette score of all the values - ax1.axvline(x=silhouette_avg, color="red", linestyle="--") - - ax1.set_yticks([]) # Clear the yaxis labels / ticks - ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1]) - - - plt.suptitle(("Silhouette analysis for clustering on sample data " - "with n_clusters = " + str(n_clusters) + "\nAverage silhouette_score = " + str(silhouette_avg)), fontsize=12, fontweight='bold') - - - plt.savefig(path, bbox_inches='tight') - -######################## dbscan ############################################## - -def dbscan(dataset, eps, min_samples): - if not os.path.exists('clustering/dbscan_output'): - os.makedirs('clustering/dbscan_output') - - if eps is not None: - clusterer = DBSCAN(eps = eps, min_samples = min_samples) - else: - clusterer = DBSCAN() - - clustering = clusterer.fit(dataset) - - core_samples_mask = np.zeros_like(clustering.labels_, dtype=bool) - core_samples_mask[clustering.core_sample_indices_] = True - labels = clustering.labels_ - - # Number of clusters in labels, ignoring noise if present. - n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0) - - silhouette_avg = silhouette_score(dataset, labels) - warning("For n_clusters =" + str(n_clusters_) + - "The average silhouette_score is :" + str(silhouette_avg)) - - ##TODO: PLOT SU DBSCAN (no centers) e HIERARCHICAL - - # Black removed and is used for noise instead. - unique_labels = set(labels) - colors = [plt.cm.Spectral(each) - for each in np.linspace(0, 1, len(unique_labels))] - for k, col in zip(unique_labels, colors): - if k == -1: - # Black used for noise. - col = [0, 0, 0, 1] - - class_member_mask = (labels == k) - - xy = dataset[class_member_mask & core_samples_mask] - plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col), - markeredgecolor='k', markersize=14) - - xy = dataset[class_member_mask & ~core_samples_mask] - plt.plot(xy[:, 0], xy[:, 1], 'o', markerfacecolor=tuple(col), - markeredgecolor='k', markersize=6) - - plt.title('Estimated number of clusters: %d' % n_clusters_) - s = 'clustering/dbscan_output/dbscan_plot.png' - fig = plt.gcf() - fig.set_size_inches(18.5, 10.5, forward = True) - fig.savefig(s, dpi=100) - - - write_to_csv(dataset, labels, 'clustering/dbscan_output/dbscan_results.tsv') - -########################## hierachical ####################################### - -def hierachical_agglomerative(dataset, k_min, k_max): - - if not os.path.exists('clustering/agglomerative_output'): - os.makedirs('clustering/agglomerative_output') - - plt.figure(figsize=(10, 7)) - plt.title("Customer Dendograms") - shc.dendrogram(shc.linkage(dataset, method='ward')) - fig = plt.gcf() - fig.savefig('clustering/agglomerative_output/dendogram.png', dpi=200) - - range_n_clusters = [i for i in range(k_min, k_max+1)] - - for n_clusters in range_n_clusters: - - cluster = AgglomerativeClustering(n_clusters=n_clusters, affinity='euclidean', linkage='ward') - cluster.fit_predict(dataset) - cluster_labels = cluster.labels_ - - silhouette_avg = silhouette_score(dataset, cluster_labels) - warning("For n_clusters =", n_clusters, - "The average silhouette_score is :", silhouette_avg) - - plt.clf() - plt.figure(figsize=(10, 7)) - plt.title("Agglomerative Hierarchical Clustering\nwith " + str(n_clusters) + " clusters and " + str(silhouette_avg) + " silhouette score") - plt.scatter(dataset[:,0], dataset[:,1], c = cluster_labels, cmap='rainbow') - s = 'clustering/agglomerative_output/hierachical_' + str(n_clusters) + '_clusters.png' - fig = plt.gcf() - fig.set_size_inches(10, 7, forward = True) - fig.savefig(s, dpi=200) - - write_to_csv(dataset, cluster_labels, 'clustering/agglomerative_output/agglomerative_hierarchical_with_' + str(n_clusters) + '_clusters.tsv') - - - - -############################# main ########################################### - - -def main(): - if not os.path.exists('clustering'): - os.makedirs('clustering') - - args = process_args(sys.argv) - - #Data read - - X = read_dataset(args.input) - X = pd.DataFrame.to_dict(X, orient='list') - X = rewrite_input(X) - X = pd.DataFrame.from_dict(X, orient = 'index') - - for i in X.columns: - tmp = X[i][0] - if tmp == None: - X = X.drop(columns=[i]) - - X = pd.DataFrame.to_numpy(X) - - - if args.cluster_type == 'kmeans': - kmeans(args.k_min, args.k_max, X, args.elbow, args.silhouette, args.davies) - - if args.cluster_type == 'dbscan': - dbscan(X, args.eps, args.min_samples) - - if args.cluster_type == 'hierarchy': - hierachical_agglomerative(X, args.k_min, args.k_max) - -############################################################################## - -if __name__ == "__main__": - main()
--- a/marea-1.0.1/marea_cluster.xml Tue Oct 01 06:03:12 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -<tool id="MaREA_cluester" name="MaREA cluster analysis" version="1.0.1"> - <description>of Reaction Activity Scores - 1.0.1</description> - <macros> - <import>marea_macros.xml</import> - </macros> - <requirements> - <requirement type="package" version="0.23.0">pandas</requirement> - <requirement type="package" version="1.1.0">scipy</requirement> - <requirement type="package" version="0.10.1">cobra</requirement> - <requirement type="package" version="0.21.3">scikit-learn</requirement> - <requirement type="package" version="2.2.2">matplotlib</requirement> - <requirement type="package" version="1.17">numpy</requirement> - </requirements> - <command detect_errors="exit_code"> - <![CDATA[ - python $__tool_directory__/marea_cluster.py - --input $input - --tool_dir $__tool_directory__ - --out_log $log - #if $data.clust_type == 'kmeans': - --k_min ${data.k_min} - --k_max ${data.k_max} - --elbow ${data.elbow} - --silhouette ${data.silhouette} - #end if - #if $data.clust_type == 'dbscan': - #if $data.dbscan_advanced.advanced == 'true' - --eps ${data.dbscan_advanced.eps} - --min_samples ${data.dbscan_advanced.min_samples} - #end if - #end if - #if $data.clust_type == 'hierarchy': - --k_min ${data.k_min} - --k_max ${data.k_max} - #end if - ]]> - </command> - <inputs> - <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> - - <conditional name="data"> - <param name="clust_type" argument="--cluster_type" type="select" label="Choose clustering type:"> - <option value="kmeans" selected="true">KMeans</option> - <option value="dbscan">DBSCAN</option> - <option value="hierarchy">Agglomerative Hierarchical</option> - </param> - <when value="kmeans"> - <param name="k_min" argument="--k_min" type="integer" min="2" max="99" value="3" label="Min number of clusters (k) to be tested" /> - <param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" /> - <param name="elbow" argument="--elbow" type="boolean" value="true" label="Draw the elbow plot from k-min to k-max"/> - <param name="silhouette" argument="--silhouette" type="boolean" value="true" label="Draw the Silhouette plot from k-min to k-max"/> - </when> - <when value="dbscan"> - <conditional name="dbscan_advanced"> - <param name="advanced" type="boolean" value="false" label="Want to use custom params for DBSCAN? (if not optimal values will be used)"> - <option value="true">Yes</option> - <option value="false">No</option> - </param> - <when value="false"></when> - <when value="true"> - <param name="eps" argument="--eps" type="float" value="0.5" label="Epsilon - The maximum distance between two samples for one to be considered as in the neighborhood of the other" /> - <param name="min_samples" argument="min_samples" type="integer" value="5" label="Min samples - The number of samples in a neighborhood for a point to be considered as a core point (this includes the point itself)"/> - - </when> - </conditional> - </when> - <when value="hierarchy"> - <param name="k_min" argument="--k_min" type="integer" min="2" max="99" value="3" label="Min number of clusters (k) to be tested" /> - <param name="k_max" argument="--k_max" type="integer" min="3" max="99" value="5" label="Max number of clusters (k) to be tested" /> - </when> - </conditional> - </inputs> - - <outputs> - <data format="txt" name="log" label="${tool.name} - Log" /> - <collection name="results" type="list" label="${tool.name} - Results"> - <discover_datasets pattern="__name_and_ext__" directory="clustering"/> - </collection> - </outputs> - <help> -<![CDATA[ - -What it does -------------- - - -]]> - </help> - <expand macro="citations" /> -</tool> - -
--- a/marea-1.0.1/marea_macros.xml Tue Oct 01 06:03:12 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -<macros> - - <xml name="options"> - <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:"> - <option value="HMRcore" selected="true">HMRcore rules</option> - <option value="Recon">Recon 2.2 rules</option> - <option value="Custom">Custom rules</option> - </param> - </xml> - - <token name="@CUSTOM_RULES_EXEMPLE@"> - -+--------------------+-------------------------------+ -| id | rule (with entrez-id) | -+====================+===============================+ -| SHMT1 | 155060 or 10357 | -+--------------------+-------------------------------+ -| NIT2 | 155060 or 100134869 | -+--------------------+-------------------------------+ -| GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 | -+--------------------+-------------------------------+ - -| - - </token> - - <token name="@DATASET_EXEMPLE1@"> - -+------------+------------+------------+------------+ -| Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 | -+============+============+============+============+ -| HGNC:24086 | 0.523167 | 0.371355 | 0.925661 | -+------------+------------+------------+------------+ -| HGNC:24086 | 0.568765 | 0.765567 | 0.456789 | -+------------+------------+------------+------------+ -| HGNC:9876 | 0.876545 | 0.768933 | 0.987654 | -+------------+------------+------------+------------+ -| HGNC:9 | 0.456788 | 0.876543 | 0.876542 | -+------------+------------+------------+------------+ -| HGNC:23 | 0.876543 | 0.786543 | 0.897654 | -+------------+------------+------------+------------+ - -| - - </token> - - <token name="@DATASET_EXEMPLE2@"> - -+-------------+------------+------------+------------+ -| Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 | -+=============+============+============+============+ -| A1BG | 0.523167 | 0.371355 | 0.925661 | -+-------------+------------+------------+------------+ -| A1CF | 0.568765 | 0.765567 | 0.456789 | -+-------------+------------+------------+------------+ -| A2M | 0.876545 | 0.768933 | 0.987654 | -+-------------+------------+------------+------------+ -| A4GALT | 0.456788 | 0.876543 | 0.876542 | -+-------------+------------+------------+------------+ -| M664Y65 | 0.876543 | 0.786543 | 0.897654 | -+-------------+------------+------------+------------+ - -| - - </token> - - <token name="@REFERENCE@"> - -This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. - -.. _BIMIB: http://sito di bio.org -.. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English -.. _University of Milan - Bicocca: https://www.unimib.it/ - - </token> - - <xml name="citations"> - <citations> <!--esempio di citazione--> - <citation type="bibtex"> -@online{lh32017, - author = {Alex Graudenzi, Davide Maspero, Cluadio Isella, Marzia Di Filippo, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani}, - year = {2018}, - title = {MaREA: Metabolic feature extraction, enrichment and visualization of RNAseq}, - publisher = {bioRxiv}, - journal = {bioRxiv}, - url = {https://www.biorxiv.org/content/early/2018/01/16/248724}, -} - </citation> - </citations> - </xml> - -</macros>