morFeus Files

Dependencies:

1. Python (tested with Python 2.6)
2. Biopython http://www.biopython.org
3. NetworkX http://networkx.github.io/
4. gnuplot http://www.gnuplot.info/
5. Graphviz http://www.graphviz.org/ (optional)
6. NCBI blast+ ftp://ftp.ncbi.nlm.nih.gov/blast/executables/
Morfeus uses BLAST against the protein sequences NCBI RefSeq database available at http://www.ncbi.nlm.nih.gov/refseq/ .

Installed and tested with Ubuntu Linux 12.04. LTS. 


To run morfeus after downloading and unpacking morfeus.tar.gz please change the following parameters in init.py:

MORFEUS_USER    = "user" 			# your user name
MORFEUS_DIR 	= "/home/user/morfeus"		# folder where morfeus is installed
QBLASTPROGRAM   = "/opt/blast/bin/blastp" 	# path to blast binary
QBLASTDATABASE  = "/opt/blast/db/refseq_protein"# path to downloaded refseq database


Running morfeus from the command line:

python morfeusd.py refseqID


Summary of Command-line Options and a short Description of their Function

Usage: morfeusd.py [options] id1 [id2 .. idn]
Options:
-h, --help show this help message and exit
-c, --cleanup (C)leanup morfeusd queue - required to clean up queue after failed job
-e EVALUE, --e-value=EVALUE (E)-value - chose the E-value for BLAST and back-BLAST jobs
-f, --file Input id (F)ile - chose Input (query); either use NCBI RefSeq ID or provide FASTA-formatted file
-g, --graph Draw network (G)raph - show network graph as output
-l, --local Use local BLAST queue - use local (as opposed to remote NCBI) BLAST queue; default: remote
-r, --re-run (R)u-run existing job - rerun a job; useful, as it saves time for back-BLASTing; enter job-ID after -r
-s, --skip (S)kip clustering (re-run) - skip the clustering step; can be used only with -r (re-run)
-n, --no-clustering (N)o clustering) - skip clustering step in new job; prevents clustering hits based on similarity of alignment and starts with back-BLASTs based on E-value