comparison scripts/functions.py @ 10:f62c76aab669 draft default tip

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1

9:04a9ada73cc4

import itertools

def simplify_fasta_name(fasta_name,LT):
    for abbreviation in LT:
        if abbreviation in fasta_name:
            new_fasta_name = abbreviation

    return(new_fasta_name)

## Generates bash, with key = fasta name; value = sequence (WITH GAP, IF ANY, REMOVED IN THIS FUNCTION)
def dico(fasta_file,LT):
    #count_fastaName = 0
    bash1 = {}
    with open(fasta_file, "r") as file:
        for name, query in itertools.izip_longest(*[file]*2):
            if not name:
                break
            if name[0] == ">":
                #count_fastaName += 1
                fasta_name = name[1:-1]
                sequence = query[:-1]
                if fasta_name not in bash1.keys():
                    fasta_name = simplify_fasta_name(fasta_name, LT)
                    bash1[fasta_name] = sequence
                else :
                    print fasta_name

    kk = bash1.keys()
    key0 = kk[0]
    seq0 = bash1[key0]
    ln_seq = len(seq0)
    
    return(bash1)

10:f62c76aab669

#!/usr/bin/env python
#coding: utf-8

import itertools, os

def dico(fasta_file, path_in):
    """
    Stores a fasta file in a dictionary : key/value -> header/sequence

    Args:
        - fasta_file (String) : the name of fasta file
        - path_in (String) : path to the fasta file

    Return:
        - bash1 (dict) : the dictionary header/sequence        
    """
    bash1 = {}    

    with open(path_in+'/'+fasta_file, 'r') as F1:
        for h,s in itertools.izip_longest(*[F1]*2):            
            fasta_name = h[1:3]
            sequence = s[:-1]
            if fasta_name not in bash1.keys():
                bash1[fasta_name] = sequence
            else:
                print fasta_name
   
    return bash1 # same length for all (alignment)

def write_output(names, sps_list, out_dir, results_dict):
    """ Write results in csv files. There is one file per counted element (one file per amino-acid, one file per indice ...)

    Args:
        - names (list) : list with the names of elems
        - sps_list (list) : species names, sorted alphabetically
        - out_dir (String) : output directory
        - results_dict (dict) : vcounts values of each element for each input file (keys names : elems from 'names argument')

    """
    for name in names:
        out = open(name+".csv", 'w')
        out.write('Group,' + sps_list[0:-1]+'\n')
        for group in results_dict.keys():
            count_of_elems = ''
            for specs in sorted(results_dict[group].keys()):
                count_of_elems += str(results_dict[group][specs][name]) + ','
            out.write(group + ',' + count_of_elems[0:-1] + '\n')
        out.close()
        os.system('mv %s.csv %s/' %(name, out_dir))

def fill_with_NaN(what):
    """ Used to create a dict only with NaN values ; used when a species is not present in an orthogroup

    Args:
        - what (list of Strings) : the names of the elements studied (nucleotide, amino-acids, indices of thermostability ...)

    Return:
        - NaN_values (dict) : dictionary with keys=elems of what, values=NaN
    """

    NaN_values = {}
    for elem in what:
        NaN_values[elem] = 'NaN'

    return NaN_values