Metadata-Version: 1.1
Name: scythe
Version: 0.1a1
Summary: Find best matching set of transcripts for one-to-one orthologous genes from two or more species
Home-page: UNKNOWN
Author: Janina Mass
Author-email: janina.mass@hhu.de
License: GPLv3
Description: =======
        Scythe
        =======
        
        *Scythe*, Selection of Conserved Transcript by Homology Evaluation, tries to find the best matching set of transcripts for each one-to-one orthologous gene from two or more species.
        
        
        Usage (GUI): ::
        	
        	scythe-gui.py
        
        
        Usage (command line): ::
            
            ######################################
            # scythe.py v0.1a1                   #
            ######################################
          usage:
             scythe.py -i DIR -g .grpFILE -d DELIMITER --cleanup
        
          usage with configuration file:
             scythe.py --config configuration.scy
        
          general options:
            -C, --config                     use configuration file instead of
                                             command line parameters
            -c, --cleanup                    remove temporary files when done
            -h, --help                       prints this
            -i, --in_dir=DIR                 folder w/ subfolders "fa" and "loc"
        
            -o, --out_dir=DIR                output directory [default:./]
            -N, --num_cores=NUM              number of processors to use [default 1]
        
         algorithm options:
            -R, --sl_ref                     find best matches to reference
            -G, --sl_glob                    best scoring pair as seed
            -M, --mx_sum                     optimize sum of pairwise scores
        
        
          alignment options:
             -O, --gap_open=FLOAT           needleall gap opening cost [default 10]
             -E, --gap_extend=FLOAT         needleall gap extension cost
        
          fasta options:
            -d, --delim=STRING               split fasta headers at STRING
            -a, --asID=INT                   use INTth part of fasta header as transcript-ID
                                             (default:0)
        
          further help:
            Please see documentation.
            
        
        Installation
        ============
        Scythe needs Python 3. You might want to set up a virtual environment with Python 3 for easier package management. 
        Please see the documentation for more details.
        (In your virtual environment) install Scythe via ::
        
            pip install scythe
        
        
        Requirements
        ============
        
        Python modules
        ~~~~~~~~~~~~~~~
        * configparser
        * mysql-connector-python
        * httplib2
        
         ::
        
            pip install configparser
            pip install --allow-external mysql-connector-python mysql-connector-python 
            pit install httplib2
        
        External programs
        ------------------
        * needleall (version 6.3.1; EMBOSS package, http://emboss.sourceforge.net/)
        
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
