view combine_metaphlan2_humann2.py @ 0:31394a0c0242 draft

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import sys
import os
import argparse
import re

def extract_clade_abundance(metaphlan2_filepath):
    clade_abundance = {}
    with open(metaphlan2_filepath, 'r') as metaphlan2_file:
        for line in metaphlan2_file.readlines():
            if line.find('g__') == -1:
                continue

            split_line = line[:-1].split('\t')
            taxo = split_line[0]
            abundance = split_line[1]

            genus = taxo[(taxo.find('g__')+3):]
            if genus.find('|') != -1:
                genus = genus[:(genus.find('|'))]
            clade_abundance.setdefault(genus, {'abundance':0, 'species':{}})
            if taxo.find('t__') != -1:
                continue
            elif taxo.find('s__') != -1:
                species = taxo[(taxo.find('s__')+3):]
                clade_abundance[genus]['species'].setdefault(species, abundance)
            else:
                clade_abundance[genus]['abundance'] = abundance
    return clade_abundance

def compute_overall_abundance(humann2_file):
    overall_abundance = 0
    with open(args.humann2_file, 'r') as humann2_file:
        for line in humann2_file.readlines():
            if line.find('|') != -1 or line.startswith('#'):
                continue
            split_line = line[:-1].split('\t')
            overall_abundance += float(split_line[1])
    return overall_abundance

def format_characteristic_name(name):
    formatted_name = name
    formatted_name = formatted_name.replace('/',' ')
    formatted_name = formatted_name.replace('-',' ')
    formatted_name = formatted_name.replace("'",'')
    if formatted_name.find('(') != -1 and formatted_name.find(')') != -1:
        open_bracket = formatted_name.find('(')
        close_bracket = formatted_name.find(')')+1
        formatted_name = formatted_name[:open_bracket] + formatted_name[close_bracket:]
    return formatted_name

def combine_metaphlan2_humann2(args):
    clade_abundance = extract_clade_abundance(args.metaphlan2_file)
    overall_abundance = compute_overall_abundance(args.humann2_file)

    with open(args.output_file, 'w') as output_file:
        output_file.write('genus\t')
        output_file.write('genus_abundance\t')
        output_file.write('species\t')
        output_file.write('species_abundance\t')
        output_file.write(args.type + '_id\t')
        output_file.write(args.type + '_name\t')
        output_file.write(args.type + '_abundance\n')
        with open(args.humann2_file, 'r') as humann2_file:
            for line in humann2_file.readlines():
                if line.find('|') == -1:
                    continue

                split_line = line[:-1].split('\t')
                abundance = 100*float(split_line[1])/overall_abundance
                annotation = split_line[0].split('|')
                characteristic = annotation[0].split(':')
                characteristic_id = characteristic[0]
                characteristic_name = ''
                if len(characteristic) > 1:
                    characteristic_name = format_characteristic_name(characteristic[-1])
                taxo = annotation[1].split('.')
                
                if taxo[0] == 'unclassified':
                    continue
                genus = taxo[0][3:]
                species = taxo[1][3:]

                if not clade_abundance.has_key(genus):
                    print "no", genus, "found in", args.metaphlan2_file
                    continue
                if not clade_abundance[genus]['species'].has_key(species):
                    print "no", species, "found in", args.metaphlan2_file,
                    print "for", genus
                    continue
                output_file.write(genus + '\t')
                output_file.write(clade_abundance[genus]['abundance'] + '\t')
                output_file.write(species + '\t')
                output_file.write(clade_abundance[genus]['species'][species] + '\t')
                output_file.write(characteristic_id + '\t')
                output_file.write(characteristic_name + '\t')
                output_file.write(str(abundance) + '\n')

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--humann2_file', required=True)
    parser.add_argument('--metaphlan2_file', required=True)
    parser.add_argument('--output_file', required=True)
    parser.add_argument('--type', required=True, 
        choices = ['gene_families','pathways'])
    args = parser.parse_args()

    combine_metaphlan2_humann2(args)