Metadata-Version: 1.1
Name: pysickle
Version: 0.1
Summary: Remove outlier sequences from multiple sequence alignment
Home-page: https://pypi.python.org/pypi/pysickle/
Author: Janina Mass
Author-email: janina.mass@hhu.de
License: GPLv3
Description: ===========
        Pysickle
        ===========
        
        **pysickle.py** will try to remove sequences that cause misalignments from a multiple sequence alignment (MSA). It reads a given MSA in multi-fasta format and removes sequences with the highest penalty scores, then builds the next MSA without those sequences. This process is repeated until a user-specified cuttoff is reached or less than three sequences are left to be aligned.
        
        Usage::
            
            ######################################
            # pysickle.py
            ######################################
            usage:
                pysickle.py -f multifasta alignment
            options:
                -f, --fasta=FILE    multifasta alignment (eg. "align.fas")
                OR
                -F, --fasta_dir=DIR directory with multifasta files (needs -s SUFFIX)
                -s, --suffix=SUFFIX will try to work with files that end with SUFFIX (eg ".fas")
        
                -a, --msa_tool=STR  supported: "mafft" [default:"mafft"]
                -i, --max_iterations=NUM    force stop after NUM iterations
                -n, --num_threads=NUM   max number of threads to be executed in parallel [default: 1]
                -m, --mode=MODE         set strategy to remove outlier sequences [default: "Sites"]
                                        available modes (not case sensitive):
                                            "Sites", "Gaps", "uGaps","Insertions",
                                            "uInsertions","uInstertionsGaps", "custom"
                -l, --log       write logfile
                -h, --help      prints this
        
            only for mode "custom":
                -g, --gap_penalty=NUM        set gap penalty [default: 1.0]
                -G, --unique_gap_penalty=NUM set unique gap penalty [default: 10.0]
                -j, --insertion_penalty=NUM  set insertion penalty [default:1.0]
                -J, --unique_insertion_penalty=NUM set insertion penalty [default:1.0]
                -M, --mismatch_penalty=NUM   set mismatch penalty [default:1.0]
                -r, --match_reward=NUM       set match reward [default: -10.0]
        
        
        Currently supported multiple sequence aligners:
        
        - mafft (Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. http://mafft.cbrc.jp/alignment/software/)
        
        
        Requirements
        ============
        * matplotlib
        * numpy
        
        External Programs
        -----------------
        * mafft
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
