/parseMethods

Parse Methods Module is a Parse Module from SEPA (a multi pipe to test pathogen software detection), that parses result files from several softwares (pathoscope, metamix, sigma, metaphlan (on development), constrains (metaphlan dependent))

Primary LanguageShellGNU General Public License v2.0GPL-2.0

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parseMethods Module

Welcome to the parseMethods module! This module takes a directory containing output files from several metagenomics software and creates a standard table (with the full lineage and read/proportions) that can be easily imported into R for downstream analyses. parseMethods is part of SEPA, a modular pipeline for testing metagenomic profiling software using simulations. Currently, parseMethods can process result files from pathoscope2, metamix, sigma, metaphlan2 (under development), and constrains (metaphlan dependent)

Requirements

Bash version 4 (comes with Linux and MacOSX) Rscript (R statistical framework) 3.0 and greater (download here) R packages rJava, methods, xlsxjars (install from R console by issuing install.packages(c("rJava", "methods", "xlsxjars")))

Usage

bash parseMethods.bash --workpath . --cfile config.conf
or
bash parseMethods.bash --workpath . --method PATHOSCOPE

Where --workpath is the path to the directory that contains your program-specific output files. In the example, the files within ./example_files/ come from PathoScope2. --cfile is a plain-text configuration file where you can pass options to the program as to what piece of software the files come from, whether you want proportions instead of reads, etc. finally --method can avoid you to use an config file just passing the method (coma separate), only valid for pathoscope2, metamix, and kraken, taxator and centrifuge.

Example output

Superkingdom Phylum Class Order Family Genus Specie Name ti ID1000-sam ID150-sam ID300-sam ID75-sam
Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus anthracis Bacillus anthracis str. CDC 684 568206 157496 155096 156413 157488
Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus anthracis Bacillus anthracis str. Ames 198094 1672 0 0 123
Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus anthracis Bacillus anthracis str. Sterne 260799 10 0 0 0
Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus anthracis Bacillus anthracis str. H9401 768494 0 0 0 1437
Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus Streptococcus pneumoniae Streptococcus pneumoniae TCH8431/19A 525381 5556 5362 5244 5266
Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus Streptococcus pneumoniae Streptococcus pneumoniae ST556 1130804 20 0 0 0
Bacteria Actinobacteria Actinobacteria Propionibacteriales Propionibacteriaceae Propionibacterium Propionibacterium acnes Propionibacterium acnes KPA171202 267747 5544 5373 5320 5504
Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus Lactobacillus crispatus Lactobacillus crispatus ST1 748671 0 5689 5586 5586
Bacteria Actinobacteria Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium Mycobacterium tuberculosis Mycobacterium tuberculosis CDC1551 83331 0 12958 12758 12946
Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus Streptococcus anginosus Streptococcus anginosus C238 862971 0 5850 5648 5887
Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus Staphylococcus epidermidis Staphylococcus epidermidis RP62A 176279 0 4349 4248 4314
Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae Lactobacillus Lactobacillus rhamnosus Lactobacillus rhamnosus ATCC 8530 1088720 0 741 624 707
Bacteria Actinobacteria Actinobacteria Propionibacteriales Propionibacteriaceae Propionibacterium Propionibacterium acnes Propionibacterium acnes 6609 1031709 0 0 0 3
Bacteria Actinobacteria Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium Mycobacterium tuberculosis Mycobacterium tuberculosis KZN 605 478435 0 0 0 164
Bacteria Actinobacteria Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium Mycobacterium tuberculosis Mycobacterium tuberculosis H37Ra 419947 0 0 0 9
Bacteria Actinobacteria Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium Mycobacterium tuberculosis Mycobacterium tuberculosis H37Rv 83332 0 0 0 2

Citation

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.
PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples Microbiome 2014 Dec 1;2(1):1-5. PMID: 25225611

Morfopoulou S, Plagnol V.
Bayesian mixture analysis for metagenomic community profiling
Bioinformatics 2015 May 21:btv317. PMID: 26002885

Ahn TH, Chai J, Pan C.
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
Bioinformatics 2014 Sep 29:btu641. PMID: 25266224

Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N.
MetaPhlAn2 for enhanced metagenomic taxonomic profiling Nature methods 2015 Oct 1;12(10):902-3. PMID: 26418763

Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D.
ConStrains identifies microbial strains in metagenomic datasets
Nature biotechnology 2015 Oct 1;33(10):1045-52. PMID: 26344404