Metadata-Version: 1.0
Name: crispor_cli
Version: 0.1.1
Summary: Command line tool for crispr offtarget finding extracted from crispor website
Home-page: https://github.com/ElucidataInc/crispor-cli
Author: Kailash Yadav
Author-email: kailash.yadav@elucidata.io
License: The source code in crispor.py and crisporEffScores.py ("the code") is under
copyright by Maximilian Haeussler maximilianh@gmail.com ("the author").

Starting with version 4, the the file crispor.py can be used freely
by academic researchers. These researchers may also modify the code and
redistribute it, provided this license file is included. Please feed back
modifications to the author.

Commercial and non-profit organisations need to contact the author to
obtain a license to run the file crispor.py or crisporEffScores.py on 
their own computer. Most non-profit organisations will be able to obtain a
license at no cost. The license for commercial users includes support 
from the author and regular updates.

All organisations can use the website crispor.org for free.

If you think these license terms make distribution of the code difficult,
please do not hesitate to contact the author.

-- 

Up to and including version 3.1, the source code files crisporEffScores.py and
crispor.py were licensed under GPLv3. See
http://www.gnu.org/licenses/gpl-3.0.en.html

Code in bin/ is under the license of the respective authors and only provided
as part of this package for installation convenience. Please see the
directories under bin/src for the exact licenses.


Description: # CRISPOR - a CRISPR/Cas9 assistant 
        
        CRISPOR predicts off-targets in the genome, ranks guides, highlights
        problematic guides, designs primers and helps with cloning.  Try it on
        http://crispr.org
        
        CRISPOR uses BWA, a few tools from the UCSC Genome Browser (twoBitToFa, bedClip),
        various R packages and a huge collection of external packages and source code files
        from published articles, see the file crisporEffScores.py for the exact references.
        
        Installation of the package:
        
            make crispor_env
        
            source crispor_env/bin/activate
        
            make devbuild
        
        Install required R libraries:
           
            sudo Rscript -e 'install.packages(c("e1071"),  repos="http://cran.rstudio.com/")'
            sudo Rscript -e 'source("https://bioconductor.org/biocLite.R"); biocLite(c("limma"));'
        
        Now in a python console type this:
        
            from crispor_cli import crispor
            
            crispor.main(args,options)
        
        Description for args and options is given below:
          args=[<genome_name>,<input_fasta>,<output_file>]
        Here args is a list containing org,fastaInFile and guideOutFile in this order:
          Example args -
            args=['sacCer3','/input/guide_yeast.fasta','/output/yo_guide.tsv']
        
        And options is a dictionary containing all the extra options permitted by crispor.
          Example options - 
            options = {'offtargetFname':'/output/yo_off.tsv','pam':'NGG','debug':True,'skipAlign':True}
        
        Here are the keys that can be added to options dictionary-
        
        Options:
          debug      -     show debug messages, do not delete temp directory
          test      -      run internal tests
          pam    -              PAM-motif to use, default NGG. TTTN triggers special
                                Cpf1 behavior: no scores anymore + the PAM is assumed
                                to be 5' of the guide. Common PAMs are:
                                NGG,TTTN,NGA,NGCG,NNAGAA,NGGNG,NNGRRT,NNNNGMTT,NNNNACA
          offtargetFname - 
                                write offtarget info to this filename
          maxOcc - 
                                MAXOCC parameter, guides with more matches are
                                excluded
        
          mismatches-
                                 maximum number of mismatches, default 4
          
          skipAlign  -
                                do not align the input sequence. The on-target will be
                                a random match with 0 mismatches.
          noEffScores -
                                do not calculate the efficiency scores
          minAltPamScore -
                                minimum MIT off-target score for alternative PAMs, default
                                1.0
          genomeDir-
                                directory with genomes, default ./genomes
        ```
            
        
        # Licenses
        
        Included software:
        
        * BWA is under GPL3
        * libSVM: under copyright by Chih-Chung Chang and Chih-Jen Lin see http://www.csie.ntu.edu.tw/~cjlin/libsvm/COPYRIGHT
        * svmlight: free for non-commercial use, see http://svmlight.joachims.org/
        * SSC: no license specified
        * primer3: GPL2.
        * Fusi/Doench score: see LICENSE.txt, (c) by Microsoft Research
        * crispor.py and crisporEffScores.py themselves are released under GPLv3, see LICENSE.txt
        
Platform: UNKNOWN
