Duke-GCB/MMAP

Name: MMAP

Owner: Duke Center for Genomic and Computational Biology

Description: Project_Lemur

Created: 2015-02-17 16:33:41.0

Updated: 2015-05-06 02:08:30.0

Pushed: 2015-05-06 02:08:30.0

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Size: 34736

Language: Python

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README

MMAP: Microbial Metagenomic Analysis Pipeline

Developing a software package to analysis metagenomics data

Language: Python 2.7 Required package

• Biopython - 1.64
• NumPy - 1.8.2
• SciPy - 0.12.1

Required software

• Genovo v0.4: http://cs.stanford.edu/group/genovo/
• Glimmer v3.02: https://ccb.jhu.edu/software/glimmer/
• requires ELPH v1.0.1: http://cbcb.umd.edu/software/ELPH/
• MINE.jar v1.0.1: http://www.exploredata.net/
• NCBI BLAST+ v2.2.28+: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Note: These software distributed here might not work with your OS!

INSTALL

Directory list

Default/Recommended folder structure. This structure is used in default control file. If Genovo/Glimmer/MINE/BLAST are located at other destination, please update the control file.

• data
• example ## contain a basic example
• Genovo
• Glimmer
• MINE
• BLAST # Contains blastx, which is a symlink to /usr/bin/blastx
• src
• core
• test

Generating local blast database

The BLAST component queries annotated Gene Ontology sequences downloaded from http://geneontology.org. Prior to running an analysis, you must download the sequences and convert them to a BLAST+ formatted database.

A bash script is provided that does this automatically: [src/scripts/makeblastdb-go.sh]. It uses curl and makeblastdb to download a FASTA-formatted protein sequence and convert it to NCBI BLAST+ format.

It accepts one argument - the output directory for the GO Sequence Database.

$ ./makeblastdb-go.sh /data/go-seqdb

After generating the local database, add its path to the control file, so that the pipeline knows where to find it.

USAGE

t the control file "data/example/control"; Update "parent_directory=" and point that to the data/ directory. Update "go_blastdb=" to point to the converted BLAST DB directory
MAP;
on src/core/main.py data/example/control

Directory list

• data
• example - testing dataset
• scripts - utilities
• src - source code
• core
• test - use unittest in Python