comparison scripts/pogs.py @ 10:1a728cb1da31 draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c

9:a76e4758dc44

    - A minimal number of species per group has to be set.

BETA VERSION
"""

import os, argparse
import numpy as np
import pandas as pd

""" Definition of a locus : header + sequence + a tag """
class Locus:    

    """ Reads an output file from the 'Pairwise' tool (AdaptSearch suite) and returns its content into a list 
        Returns a list of sets (2 items per set) """
    def getPairwiseCouple(pairwiseFile):        
        list_pairwises_2sp = []
        with open(pairwiseFile, "r") as file:
            while (1):  # Ugly !
                name, sequence, name2, sequence2 = file.readline(), file.readline(), file.readline(), file.readline()
                if not name: break # Use assert ?
                # One locus every two lines (one pairwise couple = 4 lines) : header + sequence
                locus1 = Locus(name, sequence)
                locus2 = Locus(name2, sequence2)
                group = set([])
                group.add(locus1)

10:1a728cb1da31

    - A minimal number of species per group has to be set.

BETA VERSION
"""

import os, argparse, itertools
import numpy as np
import pandas as pd

""" Definition of a locus : header + sequence + a tag """
class Locus:    

    """ Reads an output file from the 'Pairwise' tool (AdaptSearch suite) and returns its content into a list 
        Returns a list of sets (2 items per set) """
    def getPairwiseCouple(pairwiseFile):        
        list_pairwises_2sp = []
        with open(pairwiseFile, "r") as file:
            for name, sequence, name2, sequence2 in itertools.izip_longest(*[file]*4):            
                # One locus every two lines (one pairwise couple = 4 lines) : header + sequence
                locus1 = Locus(name, sequence)
                locus2 = Locus(name2, sequence2)
                group = set([])
                group.add(locus1)