Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
A scorer for TALEN binding site in genome in C++ and python
C++ Python Shell
branch: master

This branch is 6 commits ahead, 1 commit behind albertwcheng:master

Fetching latest commit…

Cannot retrieve the latest commit at this time

Failed to load latest commit information.
CppBioClasses @ 6b89a31
CppUtilClasses @ aabb06f
bedSeq @ 41c9601
.gitignore
.gitmodules
README.md
constructTALENPWM.py
findTALENPairsInGenome.py
main.cpp
make.sh
writeGenbankSequenceOnPairedHits.py

README.md

TALENPWMScorer

Dependencies

  • g++
  • python

Build

git clone https://github.com/andynu/TALENPWMScorer.git
git submodule init
git submodule update
./make.sh

Run

Usage: ./findTALENPairsInGenome.py seqDir mode1 motifDef1 modeParam1 topN1 minSpacer maxSpacer mode2 motifDef2 modeParam2 topN2 outDir
seqDir 
mode1 
  "consensus"
    provided desired bind sequence
  "PWM"
motifDef1 
  if mode1 "consensus"
    provided desired bind sequence
  if mode1 "PWM"
  filename that provides the position weight matrix
modeParam1 
  if mode1 "consensus"
    number of mismatches 
  if mode1 "PWM"
    minimum score
topN1 
  number of sites to output
minSpacer 
  number
maxSpacer 
  number
mode2
  "consensus"
    provided desired bind sequence
  "PWM"
motifDef2
  if mode2 "consensus"
    provided desired bind sequence
  if mode2 "PWM"
  filename that provides the position weight matrix
modeParam2 
  if mode2 "consensus"
    number of mismatches 
  if mode2 "PWM"
    minimum score
topN2g 
  number of sites to output
minSpacer 
  number
maxSpacer 
  number
outDir
Something went wrong with that request. Please try again.