view scripts/S01_find_orf_on_multiple_alignment.py @ 10:3d00be2d05f3 draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 7d45b8e07bf99420df9b195617515b8002b5eaf3

#!/usr/bin/python
# coding: utf8
## Author: Eric Fontanillas
## Modification: 03/09/14 by Julie BAFFARD
## Last modification : 05/03/18 by Victor Mataigne

## Description: Predict potential ORF on the basis of 2 criteria + 1 optional criteria
                ## CRITERIA 1 ## Longest part of the alignment of sequence without codon stop "*", tested in the 3 potential ORF
                ## CRITERIA 2 ## This longest part should be > 150nc or 50aa
                ## CRITERIA 3 ## [OPTIONNAL] A codon start "M" should be present in this longuest part, before the last 50 aa
                                 ## OUTPUTs "05_CDS_aa" & "05_CDS_nuc" => NOT INCLUDE THIS CRITERIA
                                 ## OUTPUTs "06_CDS_with_M_aa" & "06_CDS_with_M_nuc" => INCLUDE THIS CRITERIA

####################################################
###### DEF 2 : Create bash for genetic code ########
####################################################
###       KEY = codon
###       VALUE = Amino Acid

def code_universel(F1):
    bash_codeUniversel = {}
    with open(F1, "r") as file:
        for line in file.readlines():
            L1 = string.split(line, " ")
            length1 = len(L1)
            if length1 == 3:
                key = L1[0]
                value = L1[2][:-1]
                bash_codeUniversel[key] = value
            else:
                key = L1[0]
                value = L1[2]
                bash_codeUniversel[key] = value
    return(bash_codeUniversel)
###########################################################


######################################################################################################################
##### DEF 3 : Test if the sequence is a multiple of 3, and if not correct the sequence to become a multiple of 3 #####
######################################################################################################################
### WEAKNESS OF THAT APPROACH = I remove extra base(s) at the end of the sequence ==> I can lost a codon, when I test ORF (as I will decay the ORF)
def multiple3(seq):
    leng = len(seq)
    modulo = leng%3
    if modulo == 0:   # the results of dividing leng per 3 is an integer
        new_seq = seq
    elif modulo == 1:    # means 1 extra nc (nucleotid) needs to be removed (the remaining of modulo indicate the part which is non-dividable per 3)
        new_seq = seq[:-1]  # remove the last nc
    elif modulo == 2:  # means 2 extra nc (nucleotid) needs to be removed (the remaining of modulo indicate the part which is non-dividable per 3)
        new_seq = seq[:-2]  # remove the 2 last nc
    len1 = len(new_seq)
    return(new_seq, modulo)
##########################################################


#############################
###### DEF 4 : GET ORF ######
#############################
##- MULTIPLE SEQUENCE BASED : Based on ALIGNMENT of several sequences
##- CRITERIA1: Get the segment in the alignment with no codon stop


###### DEF 4 - Part 1 - ######
##############################
def simply_get_ORF(seq_dna, bash_codeUniversel):
    seq_aa = ""
    i = 0
    len1 = len(seq_dna)
    while i < len1:
        base1 = seq_dna[i]
        base1 = string.capitalize(base1)
        base2 = seq_dna[i+1]
        base2 = string.capitalize(base2)
        base3 = seq_dna[i+2]
        base3 = string.capitalize(base3)

        codon = base1+base2+base3
        codon = string.replace(codon, "T", "U")

        if codon in bash_codeUniversel.keys():
            aa = bash_codeUniversel[codon]
            seq_aa = seq_aa + aa
        else:
            seq_aa = seq_aa +"?"    ### Take account for gap "-" and "N"
        i = i + 3

    return(seq_aa)
##########################################################


###### DEF 4 - Part 2 - ######
##############################
def find_good_ORF_criteria_3(bash_aligned_nc_seq, bash_codeUniversel):

    ## 1 ## Get the list of aligned aa seq for the 3 ORF:
    bash_of_aligned_aa_seq_3ORF = {}
    bash_of_aligned_nuc_seq_3ORF = {}
    BEST_LONGUEST_SUBSEQUENCE_LIST_POSITION = []
    for fasta_name in bash_aligned_nc_seq.keys():
        ## 1.1. ## Get the raw sequence
        sequence_nc = bash_aligned_nc_seq[fasta_name]

        ## 1.2. ## Check whether the sequence is multiple of 3, and correct it if not:
        new_sequence_nc, modulo = multiple3(sequence_nc)                                  ### DEF 3 ###

        ## 1.3. ## Get the 3 ORFs (nuc) for each sequence
        seq_nuc_ORF1 = new_sequence_nc
        seq_nuc_ORF2 = new_sequence_nc[1:-2]
        seq_nuc_ORF3 = new_sequence_nc[2:-1]
        seq_reversed=ReverseComplement2(seq_nuc_ORF1)
        seq_nuc_ORF4=seq_reversed
        seq_nuc_ORF5=seq_reversed[1:-2]
        seq_nuc_ORF6=seq_reversed[2:-1]

        LIST_6_ORF_nuc = [seq_nuc_ORF1, seq_nuc_ORF2, seq_nuc_ORF3,seq_nuc_ORF4,seq_nuc_ORF5,seq_nuc_ORF6]
        bash_of_aligned_nuc_seq_3ORF[fasta_name] = LIST_6_ORF_nuc     ### For each seq of the multialignment => give the 6 ORFs (in nuc)

        ## 1.4. ## Get the 3 ORFs (aa) for each sequence
        seq_prot_ORF1 = simply_get_ORF(seq_nuc_ORF1,bash_codeUniversel)                ### DEF 4 - Part 1 - ##
        seq_prot_ORF2 = simply_get_ORF(seq_nuc_ORF2,bash_codeUniversel)                ### DEF 4 - Part 1 - ##
        seq_prot_ORF3 = simply_get_ORF(seq_nuc_ORF3,bash_codeUniversel)                ### DEF 4 - Part 1 - ##
        seq_prot_ORF4 = simply_get_ORF(seq_nuc_ORF4,bash_codeUniversel)                ### DEF 4 - Part 1 - ##
        seq_prot_ORF5 = simply_get_ORF(seq_nuc_ORF5,bash_codeUniversel)                ### DEF 4 - Part 1 - ##
        seq_prot_ORF6 = simply_get_ORF(seq_nuc_ORF6,bash_codeUniversel)                ### DEF 4 - Part 1 - ##

        LIST_6_ORF_aa = [seq_prot_ORF1, seq_prot_ORF2, seq_prot_ORF3,seq_prot_ORF4,seq_prot_ORF5,seq_prot_ORF6]
        bash_of_aligned_aa_seq_3ORF[fasta_name] = LIST_6_ORF_aa     ### For each seq of the multialignment => give the 6 ORFs (in aa)

    ## 2 ## Test for the best ORF (Get the longuest segment in the alignment with no codon stop ... for each ORF ... the longuest should give the ORF)
    BEST_MAX = 0
    for i in [0,1,2,3,4,5]:   ### Test the 6 ORFs
        ORF_Aligned_aa = []
        ORF_Aligned_nuc = []


        ## 2.1 ## Get the alignment of sequence for a given ORF
        ## Compare the 1rst ORF between all sequence => list them in ORF_Aligned_aa // them do the same for the second ORF, and them the 3rd
        for fasta_name in bash_of_aligned_aa_seq_3ORF.keys():
            ORFsequence = bash_of_aligned_aa_seq_3ORF[fasta_name][i]
            aa_length = len(ORFsequence)
            ORF_Aligned_aa.append(ORFsequence)   ### List of all sequences in the ORF nb "i" =

        n = i+1

        for fasta_name in bash_of_aligned_nuc_seq_3ORF.keys():
            ORFsequence = bash_of_aligned_nuc_seq_3ORF[fasta_name][i]
            nuc_length = len(ORFsequence)
            ORF_Aligned_nuc.append(ORFsequence)   ### List of all sequences in the ORF nb "i" =

        ## 2.2 ## Get the list of sublist of positions whithout codon stop in the alignment
        ## For each ORF, now we have the list of sequences available (i.e. THE ALIGNMENT IN A GIVEN ORF)
        ## Next step is to get the longuest subsequence whithout stop
        ## We will explore the presence of stop "*" in each column of the alignment, and get the positions of the segments between the positions with "*"
        MAX_LENGTH = 0
        LONGUEST_SEGMENT_UNSTOPPED = ""
        j = 0 # Start from first position in alignment
        List_of_List_subsequences = []
        List_positions_subsequence = []
        while j < aa_length:
                column = []
                for seq in ORF_Aligned_aa:
                    column.append(seq[j])
                j = j+1
                if "*" in column:
                    List_of_List_subsequences.append(List_positions_subsequence) ## Add previous list of positions
                    List_positions_subsequence = []                              ## Re-initialyse list of positions
                else:
                    List_positions_subsequence.append(j)

        ## 2.3 ## Among all the sublists (separated by column with codon stop "*"), get the longuest one (BETTER SEGMENT for a given ORF)
        LONGUEST_SUBSEQUENCE_LIST_POSITION = []
        MAX=0
        for sublist in List_of_List_subsequences:
            if len(sublist) > MAX and len(sublist) > MINIMAL_CDS_LENGTH:
                MAX = len(sublist)
                LONGUEST_SUBSEQUENCE_LIST_POSITION = sublist

        ## 2.4. ## Test if the longuest subsequence start exactly at the beginning of the original sequence (i.e. means the ORF maybe truncated)
        if LONGUEST_SUBSEQUENCE_LIST_POSITION != []:
            if LONGUEST_SUBSEQUENCE_LIST_POSITION[0] == 0:
                CDS_maybe_truncated = 1
            else:
                CDS_maybe_truncated = 0
        else:
            CDS_maybe_truncated = 0


        ## 2.5 ## Test if this BETTER SEGMENT for a given ORF, is the better than the one for the other ORF (GET THE BEST ORF)
        ## Test whether it is the better ORF
        if MAX > BEST_MAX:
            BEST_MAX = MAX
            BEST_ORF = i+1
            BEST_LONGUEST_SUBSEQUENCE_LIST_POSITION = LONGUEST_SUBSEQUENCE_LIST_POSITION


    ## 3 ## ONCE we have this better segment (BEST CODING SEGMENT)
    ## ==> GET THE STARTING and ENDING POSITIONS (in aa position and in nuc position)
    ## And get the INDEX of the best ORF [0, 1, or 2]
    if BEST_LONGUEST_SUBSEQUENCE_LIST_POSITION != []:
        pos_MIN_aa = BEST_LONGUEST_SUBSEQUENCE_LIST_POSITION[0]
        pos_MIN_aa = pos_MIN_aa - 1
        pos_MAX_aa = BEST_LONGUEST_SUBSEQUENCE_LIST_POSITION[-1]


        BESTORF_bash_of_aligned_aa_seq = {}
        BESTORF_bash_of_aligned_aa_seq_CODING = {}
        for fasta_name in bash_of_aligned_aa_seq_3ORF.keys():
            index_BEST_ORF = BEST_ORF-1  ### cause list going from 0 to 2 in LIST_3_ORF, while the ORF nb is indexed from 1 to 3
            seq = bash_of_aligned_aa_seq_3ORF[fasta_name][index_BEST_ORF]
            seq_coding = seq[pos_MIN_aa:pos_MAX_aa]
            BESTORF_bash_of_aligned_aa_seq[fasta_name] = seq
            BESTORF_bash_of_aligned_aa_seq_CODING[fasta_name] = seq_coding

        ## 4 ## Get the corresponding position (START/END of BEST CODING SEGMENT) for nucleotides alignment
        pos_MIN_nuc = pos_MIN_aa * 3
        pos_MAX_nuc = pos_MAX_aa * 3

        BESTORF_bash_aligned_nc_seq = {}
        BESTORF_bash_aligned_nc_seq_CODING = {}
        for fasta_name in bash_aligned_nc_seq.keys():
            seq = bash_of_aligned_nuc_seq_3ORF[fasta_name][index_BEST_ORF]
            seq_coding = seq[pos_MIN_nuc:pos_MAX_nuc]
            BESTORF_bash_aligned_nc_seq[fasta_name] = seq
            BESTORF_bash_aligned_nc_seq_CODING[fasta_name] = seq_coding

    else: ### no CDS found ###
        BESTORF_bash_aligned_nc_seq = {}
        BESTORF_bash_aligned_nc_seq_CODING = {}
        BESTORF_bash_of_aligned_aa_seq = {}
        BESTORF_bash_of_aligned_aa_seq_CODING ={}



    ### Check whether their is a "M" or not, and if at least 1 "M" is present, that it is not in the last 50 aa
    ###########################################################################################################

    BESTORF_bash_of_aligned_aa_seq_CDS_with_M = {}
    BESTORF_bash_of_aligned_nuc_seq_CDS_with_M = {}

    Ortho = 0
    for fasta_name in BESTORF_bash_of_aligned_aa_seq_CODING.keys():
        seq_aa = BESTORF_bash_of_aligned_aa_seq_CODING[fasta_name]
        Ortho = detect_Methionine(seq_aa, Ortho)                                ### DEF6 ###

    ## CASE 1: A "M" is present and correctly localized (not in last 50 aa)
    if Ortho == 1:
        BESTORF_bash_of_aligned_aa_seq_CDS_with_M = BESTORF_bash_of_aligned_aa_seq_CODING
        BESTORF_bash_of_aligned_nuc_seq_CDS_with_M = BESTORF_bash_aligned_nc_seq_CODING

    ## CASE 2: in case the CDS is truncated, so the "M" is maybe missing:
    if Ortho == 0 and CDS_maybe_truncated == 1:
        BESTORF_bash_of_aligned_aa_seq_CDS_with_M = BESTORF_bash_of_aligned_aa_seq_CODING
        BESTORF_bash_of_aligned_nuc_seq_CDS_with_M = BESTORF_bash_aligned_nc_seq_CODING

    ## CASE 3: CDS not truncated AND no "M" found in good position (i.e. before the last 50 aa):
        ## => the 2 bash "CDS_with_M" are left empty ("{}")

    return(BESTORF_bash_aligned_nc_seq,  BESTORF_bash_aligned_nc_seq_CODING, BESTORF_bash_of_aligned_nuc_seq_CDS_with_M, BESTORF_bash_of_aligned_aa_seq, BESTORF_bash_of_aligned_aa_seq_CODING, BESTORF_bash_of_aligned_aa_seq_CDS_with_M)
##########################################################


##################################################################################################
###### DEF 5 : Detect all indices corresponding to all occurance of a substring in a string ######
##################################################################################################
def allindices(string, sub):
    listindex=[]
    offset=0
    i = string.find(sub, offset)
    while i >= 0:
        listindex.append(i)
        i = string.find(sub, i + 1)
    return listindex
######################################################


############################################################
###### DEF 6 : Detect if methionin in the aa sequence ######
############################################################
def detect_Methionine(seq_aa, Ortho):

    ln = len(seq_aa)
    nbre = sys.argv[2]
    CUTOFF_Last_50aa = ln - MINIMAL_CDS_LENGTH
    #Ortho = 0  ## means orthologs not found

    ## Find all indices of occurances of "M" in a string of aa
    list_indices = allindices(seq_aa, "M")                  ### DEF5 ###

    ## If some "M" are present, find whether the first "M" found is not in the 50 last aa (indice < CUTOFF_Last_50aa) ==> in this case: maybenot a CDS
    if list_indices != []:
        first_M = list_indices[0]
        if first_M < CUTOFF_Last_50aa:
            Ortho = 1  ## means orthologs found

    return(Ortho)
###################################


############################################################
###### DEF 7 : Reverse complement DNA sequence ######
###### Reference: http://crazyhottommy.blogspot.fr/2013/10/python-code-for-getting-reverse.html
############################################################
def ReverseComplement2(seq):
    # too lazy to construct the dictionary manually, use a dict comprehension
    seq1 = 'ATCGN-TAGCN-atcgn-tagcn-'
    seq_dict = { seq1[i]:seq1[i+6] for i in range(24) if i < 6 or 12<=i<=16 }
    return "".join([seq_dict[base] for base in reversed(seq)])
############################


#######################
##### RUN RUN RUN #####
#######################
import string, os, time, re, zipfile, sys
from dico import dico

MINIMAL_CDS_LENGTH = int(sys.argv[2])  ## in aa number

### Get Universal Code
bash_codeUniversel = code_universel(sys.argv[1])  ### DEF2 ###

## INPUT from file containing list of species
list_files = []
with open(sys.argv[3], 'r') as f:
    for line in f.readlines():
        list_files.append(line.strip('\n'))

os.mkdir("04_BEST_ORF_nuc")
Path_OUT1 = "04_BEST_ORF_nuc"
os.mkdir("04_BEST_ORF_aa")
Path_OUT2 = "04_BEST_ORF_aa"

os.mkdir("05_CDS_nuc")
Path_OUT3 = "05_CDS_nuc"
os.mkdir("05_CDS_aa")
Path_OUT4 = "05_CDS_aa"

os.mkdir("06_CDS_with_M_nuc")
Path_OUT5 = "06_CDS_with_M_nuc"
os.mkdir("06_CDS_with_M_aa")
Path_OUT6 = "06_CDS_with_M_aa"

### Get the Bash corresponding to an alignment file in fasta format
count_file_processed = 0
count_file_with_CDS = 0
count_file_without_CDS = 0
count_file_with_CDS_plus_M = 0

# ! : Currently, files are named "Orthogroup_x_y_sequences.fasta, where x is the number of the orthogroup (not important, juste here to make a distinct name),
# and y is the number of sequences/species in the group. These files are outputs of blastalign, where species can be removed. y is then modified.

name_elems = ["orthogroup", "0", "with", "0", "species.fasta"]

# by fixing the counter here, there will be some "holes" in the outputs directories (missing numbers), but the groups between directories will correspond
#n0 = 0

for file in list_files:
    #n0 += 1

    count_file_processed = count_file_processed + 1
    nb_gp = file.split('_')[1] # Keep trace of the orthogroup number
    fasta_file_path = "./%s" %file    
    bash_fasta = dico(fasta_file_path)   ### DEF 1 ###    
    BESTORF_nuc, BESTORF_nuc_CODING, BESTORF_nuc_CDS_with_M, BESTORF_aa, BESTORF_aa_CODING, BESTORF_aa_CDS_with_M  = find_good_ORF_criteria_3(bash_fasta, bash_codeUniversel)   ### DEF 4 - PART 2 - ###
    
    name_elems[1] = nb_gp

    ## a ## OUTPUT BESTORF_nuc
    if BESTORF_nuc != {}:
        name_elems[3] = str(len(BESTORF_nuc.keys()))
        new_name = "_".join(name_elems)
        count_file_with_CDS = count_file_with_CDS +1
        OUT1 = open("%s/%s" %(Path_OUT1,new_name), "w")
        for fasta_name in BESTORF_nuc.keys():
            seq = BESTORF_nuc[fasta_name]
            OUT1.write("%s\n" %fasta_name)
            OUT1.write("%s\n" %seq)
        OUT1.close()
    else:
        count_file_without_CDS = count_file_without_CDS + 1

    ## b ## OUTPUT BESTORF_nuc_CODING  ===> THE MOST INTERESTING!!!
    if BESTORF_aa != {}:
        name_elems[3] = str(len(BESTORF_aa.keys()))
        new_name = "_".join(name_elems)
        OUT2 = open("%s/%s" %(Path_OUT2,new_name), "w")
        for fasta_name in BESTORF_aa.keys():
            seq = BESTORF_aa[fasta_name]
            OUT2.write("%s\n" %fasta_name)
            OUT2.write("%s\n" %seq)
        OUT2.close()

    ## c ## OUTPUT BESTORF_aa
    if BESTORF_nuc_CODING != {}:
        name_elems[3] = str(len(BESTORF_nuc_CODING.keys()))
        new_name = "_".join(name_elems)
        OUT3 = open("%s/%s" %(Path_OUT3,new_name), "w")
        for fasta_name in BESTORF_nuc_CODING.keys():
            seq = BESTORF_nuc_CODING[fasta_name]
            OUT3.write("%s\n" %fasta_name)
            OUT3.write("%s\n" %seq)
        OUT3.close()

    ## d ## OUTPUT BESTORF_aa_CODING
    if BESTORF_aa_CODING != {}:
        name_elems[3] = str(len(BESTORF_aa_CODING.keys()))
        new_name = "_".join(name_elems)
        OUT4 = open("%s/%s" %(Path_OUT4,new_name), "w")
        for fasta_name in BESTORF_aa_CODING.keys():
            seq = BESTORF_aa_CODING[fasta_name]
            OUT4.write("%s\n" %fasta_name)
            OUT4.write("%s\n" %seq)
        OUT4.close()

    ## e ## OUTPUT BESTORF_nuc_CDS_with_M
    if BESTORF_nuc_CDS_with_M != {}:
        name_elems[3] = str(len(BESTORF_nuc_CDS_with_M.keys()))
        new_name = "_".join(name_elems)
        count_file_with_CDS_plus_M = count_file_with_CDS_plus_M + 1
        OUT5 = open("%s/%s" %(Path_OUT5,new_name), "w")
        for fasta_name in BESTORF_nuc_CDS_with_M.keys():
            seq = BESTORF_nuc_CDS_with_M[fasta_name]
            OUT5.write("%s\n" %fasta_name)
            OUT5.write("%s\n" %seq)
        OUT5.close()

    ## f ## OUTPUT BESTORF_aa_CDS_with_M
    if BESTORF_aa_CDS_with_M != {}:
        name_elems[3] = str(len(BESTORF_aa_CDS_with_M.keys()))
        new_name = "_".join(name_elems)
        OUT6 = open("%s/%s" %(Path_OUT6,new_name), "w")
        for fasta_name in BESTORF_aa_CDS_with_M.keys():
            seq = BESTORF_aa_CDS_with_M[fasta_name]
            OUT6.write("%s\n" %fasta_name)
            OUT6.write("%s\n" %seq)
        OUT6.close()

    #os.system("rm -rf %s" %file)

## Print
print "*************** CDS detection ***************"
print "\nFiles processed: %d" %count_file_processed
print "\tFiles with CDS: %d" %count_file_with_CDS
print "\t\tFiles with CDS plus M (codon start): %d" %count_file_with_CDS_plus_M
print "\tFiles without CDS: %d \n" %count_file_without_CDS
print ""