Mapp 0.1.0

Prerequisites

You have to install:

• Python 2.7

• MAPP program.

• Optionally download fasta database (or it is possible to use HMMER or BLAST program remotely).

• Install program for sequence searching. Recommended is HMMER. Or it is possible to download BLAST.

• Install multiple sequence alignment program (recommended is MAFFT).

• Install phylogenetic tree construction program (recommended is FastTree).

• Install Biopython package (if you want to use file convert tools).

Settings File

For MAPP analysis settings file is needed (in python ConfigParser syntax).

Settings file contains commands and input/output of commands. One command should be one basic shell command (semicolon etc. are not allowed).

Settings file could be easilly created by another script and then is easy to run multiple mapp analysis at once.

Basic and minimal required structer for settings.conf is:

[commands]
#id used for name of analysis
id=
#sequence file in fasta format
sequence =
#output file from blast or hmmer program
blastout =
#file where programs store stats about sequence picking
blaststat =
# blast command to run
blast =
# input file for multiple sequence aligning program (same as blast output)
msain = %(blastout)s
# msa program output file
msaout =
# this command is executed before msa program is executed
# (it could be for blast output conversion and purifying)
beforemsa =
# msa program command
msa =
# tree program input file (converted msaout file to newick format)
treein =
# tree program output file
treeout =
# this command is executed before the tree program
beforetree =
# tree program command
tree =
# mapp program input msa file (in fasta format - could be the same as msaout value)
mappinmsa =
# mapp program input tree file (in newick format)
mappintree =
# mapp program output file
mappout =
# command before the mapp command (good for e.g. adjust tree to proper newick format)
# MAPP is really sensitive to proper file format
beforemapp =
# MAPP command itself
mapp = java -jar MAPP.jar -f %(mappinmsa)s -t %(mappintree)s -o %(mappout)s

Basic usage in python program

Basic python code:

from mapp.core.analyzers import Analyzer
from mapp.core.parsers import SettingsParser
from mapp.core.exceptions import MappError

settings_file = 'settings.conf'

def main():
    try:
        mapp = Analyzer(SettingsParser(settings_file))
        mapp.exec_mapp()
    except MappError as e:
        print(e.header)
        print(e.description)

if __name__ == '__main__':
    main()

Helper files

In the mapp.utils package are files that can be use as standalone scripts or as modules. This file mostly serves for file conversions and purifying.