comparison scripts/functions.py @ 8:471ed956ff13 draft

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

7:f1ee838a8966

import string

# Used in S05 and
def split_file(path_in, keyword):

    file_in = open(path_in, "r")    

    list_informations=[length_matched, Expect, Score, identities, hits, identity_percent, divergence_percent,gaps_number, real_divergence_percent, frame, length_matched]

    return(list_informations)

# Used in S06, S09, S11
def get_pairs(fasta_file_path):
    F2 = open(fasta_file_path, "r")
    list_pairwises = []
    while 1:
        next2 = F2.readline()
        if not next2:
            break
        if next2[0] == ">":
            fasta_name_query = next2[:-1]
            next3 = F2.readline()
            fasta_seq_query = next3[:-1]
            next3 = F2.readline()    ## jump one empty line (if any after the sequence)
            fasta_name_match = next3[:-1]
            next3 = F2.readline()
            fasta_seq_match = next3[:-1]
            pairwise = [fasta_name_query,fasta_seq_query,fasta_name_match,fasta_seq_match]
            
            ## ADD pairwise with condition
            list_pairwises.append(pairwise)
    F2.close()
    
    return(list_pairwises)

def extract_length(length_string):   # format length string = 57...902
    l3 = string.split(length_string, "...")
    n1 = string.atoi(l3[0])

8:471ed956ff13

import string, itertools

# Used in S05 and
def split_file(path_in, keyword):

    file_in = open(path_in, "r")    

    list_informations=[length_matched, Expect, Score, identities, hits, identity_percent, divergence_percent,gaps_number, real_divergence_percent, frame, length_matched]

    return(list_informations)

# Used in S06, S09, S11
def get_pairs(fasta_file_path):    
    list_pairwises = []
    with open(fasta_file_path, "r") as F2:
        for name, sequence, name2, sequence2 in itertools.izip_longest(*[F2]*4):            
            if name[0] == ">":
                fasta_name_query = name[:-1]                
                fasta_seq_query = sequence[:-1]                
                fasta_name_match = name2[:-1]                
                fasta_seq_match = sequence2[:-1]
                pairwise = [fasta_name_query,fasta_seq_query,fasta_name_match,fasta_seq_match]
                
                ## ADD pairwise with condition
                list_pairwises.append(pairwise)
    return(list_pairwises)

def extract_length(length_string):   # format length string = 57...902
    l3 = string.split(length_string, "...")
    n1 = string.atoi(l3[0])