Metadata-Version: 2.1
Name: fishlifeqc
Version: 0.8.0
Summary: UNKNOWN
Home-page: https://github.com/Ulises-Rosas/fishlifeqc
Author: Ulises Rosas
License: UNKNOWN
Description: # fishlifeqc
        
        Features:
        
        - [x] quality control for exon alignments
        
        Software requierements:
        
        * pip
        * git
        
        ## Installation
        
        Get the development version:
        
        ```Bash
        git clone https://github.com/Ulises-Rosas/fishlifeqc.git && cd fishlifeqc
        python3 -m pip install .
        ```
        
        ## Usage
        
        Main command:
        ```Bash
        fishlifeqc -h
        ```
        
        ```
        usage: fishlifeqc [-h] {mdata,rblast,bold,tlike,bl,para,srh} ...
        
                                         Quality Control Steps
                                              
        
        positional arguments:
          {mdata,rblast,bold,tlike,bl,para,srh}
            mdata               Trim sequences in function of gap ocurrences
            rblast              Reciprocal blastn comparing taxonomical groups
            bold                Match sequences against the BOLD database
            tlike               Find T-like clades in trees
            bl                  Branch length ratios and correlations
            para                Test paraphyly with AU tests
            srh                 Test stationarity, reversibility and homogeneity
        
        optional arguments:
          -h, --help            show this help message and exit
        ```
        
        Utilities command:
        ```Bash
        qcutil -h
        ```
        
        ```
        usage: qcutil [-h] {qstats,fstats,itt,rf,delete,knockdown} ...
        
                                         Utilities from fishlifeqc
                                              
        
        positional arguments:
          {qstats,fstats,itt,rf,delete,knockdown}
            qstats              quick summary of alignment information
            fstats              full summary of both alignment and tree information
            itt                 Incongruence through time
            rf                  Robinson-Foulds distances
            delete              Delete specific sequences from files
            knockdown           Replace specific codon positions with gaps
        
        optional arguments:
          -h, --help            show this help message and exit
        ```
        
        Yet unintegrated scripts into `qcutil`:
        
        * `merge.py` : join two set of exons by using a map file
        * `concatenate.py` : concatenate exons
        * `codon_partition.py` : generate a condon partition file
        * `cons_trees.py` : for each exon, constrain a reference tree by exon taxa
        * `collapse.py` : collapse edges in function of support values
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
