changeset 0:035a848cb73e draft

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_humann2_output.py	Tue Apr 12 02:56:13 2016 -0400
@@ -0,0 +1,138 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+import argparse
+import re
+
+def extract_abundances(filepath, nb_charact_to_extract):
+    abundances = {}
+    more_abund_charact = []
+    abund_sum = 0
+    with open(filepath, 'r') as abundance_file:
+        for line in abundance_file.readlines()[1:]:
+            split_line = line[:-1].split('\t')
+            charact_id = split_line[0]
+            abund = float(split_line[1])
+            abundances[charact_id] = 100*abund
+            abund_sum += abundances[charact_id]
+
+            if len(more_abund_charact) < nb_charact_to_extract:
+                more_abund_charact.append(charact_id)
+            else:
+                best_pos = None
+                for i in range(len(more_abund_charact)-1,-1,-1):
+                    if abundances[more_abund_charact[i]] < abund:
+                        best_pos = i
+                    else:
+                        break
+                if best_pos != None:
+                    tmp_more_abund_charact = more_abund_charact
+                    more_abund_charact = tmp_more_abund_charact[:best_pos]
+                    more_abund_charact += [charact_id]
+                    more_abund_charact += tmp_more_abund_charact[best_pos:-1]
+    return abundances, more_abund_charact
+
+def format_characteristic_name(all_name):
+    if all_name.find(':') != -1:
+        charact_id = all_name.split(':')[0]
+        charact_name = all_name.split(':')[1][1:]
+    else:
+        charact_id = all_name
+        charact_name = ''
+
+    charact_name = charact_name.replace('/',' ')
+    charact_name = charact_name.replace('-',' ')
+    charact_name = charact_name.replace("'",'')
+    if charact_name.find('(') != -1 and charact_name.find(')') != -1:
+        open_bracket = charact_name.find('(')
+        close_bracket = charact_name.find(')')+1
+        charact_name = charact_name[:open_bracket] + charact_name[close_bracket:]
+    return charact_id,charact_name
+
+def write_more_abundant_charat(abundances,more_abund_charact, output_filepath):
+    with open(output_filepath,'w') as output_file:
+        output_file.write('id\tname\t')
+        output_file.write('\t'.join(abundances.keys()) + '\n')
+
+        for mac in more_abund_charact:
+            charact_id,charact_name = format_characteristic_name(mac)
+            output_file.write(charact_id + '\t' + charact_name)
+            for sample in abundances:
+                abund = abundances[sample].get(mac, 0)
+                output_file.write('\t' + str(abund))
+            output_file.write('\n')
+
+def extract_similar_characteristics(abundances, sim_output_filepath,
+    specific_output_files):
+    sim_characteristics = set(abundances[abundances.keys()[0]].keys())
+    for sample in abundances.keys()[1:]:
+        sim_characteristics.intersection_update(abundances[sample].keys())
+    print 'Similar between all samples:', len(sim_characteristics)
+
+    with open(sim_output_filepath, 'w') as sim_output_file:
+        sim_output_file.write('id\tname\t' + '\t'.join(abundances.keys()) + '\n')
+        for charact in list(sim_characteristics):
+            charact_id,charact_name = format_characteristic_name(charact)
+            sim_output_file.write(charact_id + '\t' + charact_name)
+            for sample in abundances.keys():
+                sim_output_file.write('\t' + str(abundances[sample][charact]))
+            sim_output_file.write('\n')
+
+    print 'Specific to samples:'
+    diff_characteristics = {}
+    for i in range(len(abundances.keys())):
+        sample = abundances.keys()[i]
+        print ' ', sample, ""
+        print '    All:', len(abundances[sample].keys())
+        diff_characteristics[sample] = set(abundances[sample].keys())
+        diff_characteristics[sample].difference_update(sim_characteristics)
+        print '    Number of specific characteristics:', 
+        print len(diff_characteristics[sample])
+        print '    Percentage of specific characteristics:',
+        print 100*len(diff_characteristics[sample])/(1.*len(abundances[sample].keys()))
+
+        relative_abundance = 0
+        with open(specific_output_files[i], 'w') as output_file:
+            output_file.write('id\tname\tabundances\n')
+            for charact in list(diff_characteristics[sample]):
+                charact_id,charact_name = format_characteristic_name(charact)
+                output_file.write(charact_id + '\t' + charact_name + '\t')
+                output_file.write(str(abundances[sample][charact]) + '\n')
+                relative_abundance += abundances[sample][charact]
+        print '    Relative abundance of specific characteristics(%):', relative_abundance
+
+    return sim_characteristics
+
+def compare_humann2_output(args):
+    abundances = {}
+    more_abund_charact = []
+
+    for i in range(len(args.sample_name)):
+        abundances[args.sample_name[i]], mac = extract_abundances(args.charact_input_file[i],
+            args.most_abundant_characteristics_to_extract)
+        more_abund_charact += mac
+
+    write_more_abundant_charat(abundances, list(set(more_abund_charact)), 
+        args.more_abundant_output_file)
+    sim_characteristics = extract_similar_characteristics(abundances, 
+        args.similar_output_file, args.specific_output_file)
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--sample_name', required=True, action='append')
+    parser.add_argument('--charact_input_file', required=True, action='append')
+    parser.add_argument('--most_abundant_characteristics_to_extract', required=True,
+        type = int)
+    parser.add_argument('--more_abundant_output_file', required=True)
+    parser.add_argument('--similar_output_file', required=True)
+    parser.add_argument('--specific_output_file', required=True,action='append')
+    args = parser.parse_args()
+
+    if len(args.sample_name) != len(args.charact_input_file):
+        raise ValueError("Same number of values (in same order) are expected for --sample_name and --charact_input_file")
+    if len(args.sample_name) != len(args.specific_output_file):
+        raise ValueError("Same number of values (in same order) are expected for --sample_name and --specific_output_file")
+
+    compare_humann2_output(args)
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_humann2_output.xml	Tue Apr 12 02:56:13 2016 -0400
@@ -0,0 +1,69 @@
+<tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0">
+    <description>and extract information</description>
+
+    <requirements>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+
+    <version_command></version_command>
+
+    <command><![CDATA[
+        mkdir specifics 
+        &&
+
+        python $__tool_directory__/compare_humann2_output.py
+            #for $sample in $samples:
+                --sample_name "${sample.sample_name}"
+                --charact_input_file "${sample.input}"
+                --specific_output_file "specifics/specific_to_${sample.sample_name}.txt"
+            #end for
+
+            --most_abundant_characteristics_to_extract $charact_nb
+            --more_abundant_output_file $more_abundant_output_file
+            --similar_output_file $similar_output_file
+            > $log
+                
+    ]]></command>
+
+    <inputs>
+        <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" >
+            <param name="sample_name" type="text" label="Name of the sample" help="(--sample_name)"/>
+            <param name="input" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization, --charact_input_file)"/>
+        </repeat>
+
+        <param name="charact_nb" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample" help="(--most_abundant_characteristics_to_extract)"/>
+    </inputs>
+
+    <outputs>
+        <data name="more_abundant_output_file" format="tabular"
+            label="${tool.name} on ${on_string}: More abundant characteristics for each sample" />
+        <data name="similar_output_file" format="tabular"
+            label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" />
+        <data name="log" format="txt"
+            label="${tool.name} on ${on_string}: Log" />
+        <collection name="specific_files" type="list">
+            <discover_datasets pattern="__designation_and_ext__" directory="specifics"/>
+        </collection>
+
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        This tool compare HUMANnN2 outputs with gene families or pathways relative abundances of several samples and extract several files:
+
+        - Similar gene families or pathways between the samples and the relative abundances and these similar characteristics
+        - Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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