GitHub - armintoepfer/OligoMatcher: OligoMatcher finds all genes, which are target of an oligo.

armintoepfer / OligoMatcher Public

Notifications You must be signed in to change notification settings
Fork 0
Star 0

OligoMatcher finds all genes, which are target of an oligo.

Notifications

Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
src		src
.gitignore		.gitignore
COPYING		COPYING
README		README

Repository files navigation

OligoMatcher finds all genes, which are target of an oligo.

#INPUT/OUTPUT:
Input files are multiple fasta files.
Output is STDOUT.

#OUTPUT FORMAT:
oligoIdentifier1;gene1;gene4;gene9;
oligoIdentifier2;gene4;gene7;

#PREREQUISITES TO RUN:
 - JAVA 7 (http://jdk7.java.net/)

#USAGE:
java -jar OligoMatcher.jar [options...]

 ------------------------
 === GENERAL options ===
  -i PATH		: Path to the oligo file (FASTA or FASTQ format) [REQUIRED]
  -g PATH		: Path to the genes file (FASTA format) [REQUIRED]
  -K int		: Size of the kmer [REQUIRED]
  -verbose		: Print debug information
 ------------------------

Example: java -jar OligoMatcher.jar -i seed.fasta -g genes.fa -K 8

#CONTACT:
 Armin Töpfer
 armin.toepfer (at) gmail.com
 http://www.bsse.ethz.ch/cbg/people/toepfera

#PREREQUISITES COMPILE (only for dev):
 - Maven 3 (http://maven.apache.org/)

#INSTALL (only for dev):
 cd OligoMatcher
 mvn OligoMatcher package
 java -jar OligoMatcher/target/OligoMatcher.jar --help

#LICENSE:
 GNU GPLv3 http://www.gnu.org/licenses/gpl-3.0