inference.py

from Graph_gff import Features,load_intersect
from Functions import get_segment_sequence,convert_strand

target_genome_name="genome2_chr10"
pos_seg=target_genome_name+".bed"
var_file=target_genome_name+"_variations.txt"
gfa="graph.gfa"
intersect_path='intersect.bed'
load_intersect(intersect_path)




# présent dans Fuctions.py mais relou à importer ?
def get_segments_sequence_and_paths(gfa): # creates two dict with the sequences of the graph's segments, and the paths 
    file_gfa=open(gfa,'r')
    lines_gfa=file_gfa.readlines()
    file_gfa.close()
    seg_seq={}
    paths={}
    for line in lines_gfa:
        line=line.split()
        if (line[0]=="S"): # get the sequence of the segment
            seg_id='s'+line[1]
            seg_seq[seg_id]=line[2]

        if (line[0]=="W") & (line[1]!="_MINIGRAPH_"): # get the walk of the genome
            
            path=line[6].replace(">",";>")
            path=path.replace("<",";<").split(';')
            list_path=[]
            for segment in path:
                if segment[0:1]=='>':
                    list_path.append('+s'+segment[1:])
                elif segment[0:1]=='<':
                    list_path.append('-s'+segment[1:])
 
            paths[line[3]]=list_path
    return [paths,seg_seq]

# présent dans Fuctions.py mais relou à importer ?
def get_segments_positions_on_genome(pos_seg): # creates a dict with the position of the segments on the target genome
    bed=open(pos_seg,'r')
    lines=bed.readlines() # read line by line ?
    bed.close()
    segments_on_target_genome={}
    for line in lines:
        line=line.split()
        [seg,chrom,start,stop,strand]=[line[3][1:],line[0],line[1],line[2],line[3][0:1]]
        segments_on_target_genome[seg]=[chrom,start,stop,strand]
    return segments_on_target_genome

def add_feature_sequence(feature,seg_seq): # add the feature's sequence in the Feature object
    feature_sequence=""
    for segment in feature.segments_list:
        if segment==feature.segments_list[0]:
            feature_sequence+=get_segment_sequence(seg_seq,segment)[feature.pos_start-2:] # revérifier les +/- 1 pour la position, avec de vraies données
        elif segment==feature.segments_list[-1]:
            feature_sequence+=get_segment_sequence(seg_seq,segment)[0:feature.pos_stop] # revérifier les +/- 1 pour la position, avec de vraies données
        else:
            feature_sequence+=get_segment_sequence(seg_seq,segment)
    feature.sequence=feature_sequence

def get_first_seg(list_seg,segments_on_target_genome): # get the first segment of the list that is in the target genome
    first_seg_found=''
    for segment in list_seg:
        if segment[1:] in segments_on_target_genome:
            first_seg_found=segment[1:]
            break
    return first_seg_found

def get_feature_path(paths,first_seg,last_seg):# find the feature's path in the target genome
    first_strand=convert_strand(segments_on_target_genome[first_seg][3])
    first_seg_stranded=first_strand+first_seg
    last_strand=convert_strand(segments_on_target_genome[last_seg][3])
    last_seg_stranded=last_strand+last_seg
    index_first_seg=int(paths[target_genome_name].index(first_seg_stranded))
    index_last_seg=int(paths[target_genome_name].index(last_seg_stranded))
    first_index=min(index_first_seg,index_last_seg)
    last_index=max(index_last_seg,index_first_seg)
    list_segfeat_azu=paths[target_genome_name][first_index:last_index+1]
    list_segfeat_azu_corrected=[convert_strand(segment_stranded[0])+segment_stranded[1:] for segment_stranded in list_segfeat_azu]
    return list_segfeat_azu_corrected

def get_rna(dna_sequence):
    return dna_sequence.replace("T","U")

def get_aa(rna_codon): # gives the aa coded by the rna codon
    match rna_codon[0:2]:
        case "UU":
            if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
                return "Phe"
            else:
                return "Leu"
        case "UC":
            return "Ser"
        case "UA":
            if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
                return "Tyr"
            else:
                return "*"
        case "UG":
            if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
                return "Cys"
            elif rna_codon[2]=="A":
                return "*"
            else:
                return "Trp"
        case "CU":
            return "Leu"
        case "CC":
            return "Pro"
        case "CA":
            if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
                return "His"
            else:
                return "Gln"
        case "CG":
            return "Arg"
        case "AU":
            if rna_codon[2]=="G":
                return "Met"
            else:
                return "Ile"
        case "AC":
            return "Thr"
        case "AA":
            if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
                return "Asn"
            else:
                return "Lys"
        case "AG":
            if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
                return "Ser"
            else:
                return "Arg"
        case "GU":
            return "Val"
        case "GC":
            return "Ala"
        case "GA":
            if (rna_codon[2]=="U") | (rna_codon[2]=="C"):
                return "Asp"
            else:
                return "Glu"
        case "GG":
            return "Gly"

from textwrap import wrap
def cut_codon(sequence):
    return wrap(sequence,3)

def traduction(sequence_arn): # translate rna
    list_codons=cut_codon(sequence_arn)
    prot=list()
    for codon in list_codons:
        if len(codon)==3:
            prot.append(get_aa(codon))
        else:
            print("attempt to get the amino acid for an incomplete codon")
    return prot

def get_sequence_on_genome(feature,segments_on_target_genome): # returns the sequence of the feature on the target genome
    list_seg=Features[feature].segments_list
    first_seg=get_first_seg(list_seg,segments_on_target_genome)
    last_seg=get_first_seg(reversed(list_seg),segments_on_target_genome)
    path_on_target=get_feature_path(paths,first_seg,last_seg)

    new_sequence=""
    for segment in path_on_target:
        if segment==cds.segments_list[0]:
            new_sequence+=get_segment_sequence(seg_seq,segment)[cds.pos_start-2:]
        elif segment==cds.segments_list[-1]:
            new_sequence+=get_segment_sequence(seg_seq,segment)[0:cds.pos_stop]
        else:
            new_sequence+=get_segment_sequence(seg_seq,segment)
    return new_sequence

def get_cds_variations(var_file): # creates dict : cds_id -> list of variations from the var file 
    var=open(var_file,'r')
    lines=var.readlines()
    var.close()

    # dict cds-var
    cds_var={}
    for line in lines:
        line=line.split()
        if line[1]=="CDS":
            cds_id=line[0].replace('.','_').replace(':','_')
            if cds_id not in cds_var.keys():
                cds_var[cds_id]=list()
            cds_var[cds_id].append(line)
    return cds_var

import re
def findOtherStart(cds,segments_on_target_genome): # look for another start codon, before or after the original one 
    print("\nlooking for a new start codon:")
    frame_shift=0
    # chercher codon start en amont du cds, dans le mrna
    seq_parent=get_sequence_on_genome(cds.parent,segments_on_target_genome)
    seq_cds=get_sequence_on_genome(cds_id,segments_on_target_genome)
    sequence_amont=seq_parent[0:seq_parent.rfind(seq_cds)] # get the mrna sequence before the last occurence of the cds sequence
    print("sequence before the CDS in the mRNA:",sequence_amont)
    if "ATG" in sequence_amont:
        start_pos_list=[m.start() for m in re.finditer('(?=ATG)', sequence_amont)]
        stop_pos_list=[m.start() for m in re.finditer('(?=TAG|TAA|TGA)', sequence_amont)]
        print("start codons position:",start_pos_list,"stop codons position:",stop_pos_list,"before the CDS") # positions (overlapping) où on trouve un atg.
        # vérifier ensuite s'il y a un stop après un atg, et sinon le cadre de lecture de l'atg (peut décaler toute la prot !)
        print("checking if there is a stop codon after the start codons in the same reading frame:")
        for start_pos in start_pos_list:
            start_pos_frame=start_pos%3
            n=len(sequence_amont)-start_pos+1
            if True not in ( (stop_pos%3==start_pos_frame) & (stop_pos>start_pos) for stop_pos in stop_pos_list) :
                #print("codon start candidat trouvé dans l'arn messager,",n,"bases en amont du cds")
                # calculer le décalage : si on en trouve un 2 bases en amont, ça décale le cadre de lecture !
                frame_shift=(frame_shift+n)%3 # vérifier le frame shift !!
                print("the start codon at the position",start_pos,",",n,"bases before the CDS, doesn't have a stop codon after in the same reading frame")
            else:
                print("the start codon at the position",start_pos,",",n,"bases before the CDS, has a stop codon after in the same reading frame")

    # chercher codon start en aval, dans le cds
    if "ATG" in seq_cds:
        start_pos_list=[m.start() for m in re.finditer('(?=ATG)', seq_cds)]
        print("start codon candidate found later in the CDS, at the base",start_pos_list[0]) # print seulement le premier
    print("\n")
    return frame_shift

def print_variation_change(deleted_sequence,inserted_sequence): # print the consequence of the variation represented by the insertion and deletion
    stop=False
    deleted_aa=traduction(get_rna(deleted_sequence))
    inserted_aa=traduction(get_rna(inserted_sequence))

    if (len(deleted_aa)!=0) & (len(inserted_aa)!=0):
        if deleted_aa!=inserted_aa:
            print("consequence :",",".join(deleted_aa),"changes into",",".join(inserted_aa))
        else:
            print("consequence : synonymous variation in",",".join(deleted_aa))
    elif len(inserted_aa)!=0:
        print("consequence : insertion of",",".join(inserted_aa))
    else:
        print("consequence : deletion of",",".join(deleted_aa))
    if ("*" in inserted_aa):
        print("stop codon apparition in the cds of the target genome")
        stop=True
    return stop


[paths,seg_seq]=get_segments_sequence_and_paths(gfa)
segments_on_target_genome=get_segments_positions_on_genome(pos_seg)
cds_var=get_cds_variations(var_file)
for feature in Features.values(): # add the sequence of all features
    add_feature_sequence(feature,seg_seq)


# analysing the variations for all the cds :
for cds_id in cds_var.keys():
    cds=Features[cds_id]
    print("analysis of the variations in the CDS",cds_id,":\n")
    frame_shift=0
    for index, var in enumerate(cds_var[cds_id]): # for each variation in the current cds :
        type_var=var[8]
        if type_var!="no_var": # if there is a variation
            posVar=[int(var[12]),int(var[13])]
            sequence_target=get_sequence_on_genome(cds_id,segments_on_target_genome)

            if type_var=="insertion":
                length_ref=0
            else:
                length_ref=len(var[9])
            if type_var=="deletion":
                length_alt=0
            else:
                length_alt=len(var[10])
            
            print("variation",index+1, ":")
            
            if posVar[0]<=3:
                print("variation of the start codon, mRNA most likely wont be translated")
                #findOtherStart(cds,segments_on_target_genome) # for now we don't look for another start codon
                break

            if abs(length_alt-length_ref)%3 == 0: # size diff 3k -> no frame shift.

                if (posVar[0])%3==0: #size diff 3k, position 3k
                    print("variation between two codons not causing a frameshift")
                    if type_var=="insertion":
                        print("insertion of",var[10])
                    elif type_var=="deletion":
                        print("deletion of",var[9])
                    else:
                        print("substitution of",var[9],"by",var[10])

                    len_fragment_after=(3-length_ref)%3
                    deleted_sequence=cds.sequence[posVar[0]:posVar[0]+length_ref+len_fragment_after]
                    inserted_sequence=sequence_target[posVar[1]:posVar[1]+length_alt+len_fragment_after]
                    stop=print_variation_change(deleted_sequence,inserted_sequence)
                    if stop:
                        break

                else: # size diff 3k, position !=3k
                    print("variation in the middle of a codon not causing a frameshift")
                    if type_var=="insertion":
                        print("insertion of",var[10])
                    elif type_var=="deletion":
                        print("deletion of",var[9])
                    else:
                        print("substitution of",var[9],"by",var[10])

                    len_fragment_before=(posVar[0])%3
                    len_fragment_after=(3-(len_fragment_before+length_ref))%3

                    total_ins=sequence_target[posVar[1]-len_fragment_before:posVar[1]+length_alt+len_fragment_after]
                    total_del=cds.sequence[posVar[0]-len_fragment_before:posVar[0]+length_ref+len_fragment_after]

                    stop=print_variation_change(total_del,total_ins)
                    if stop:
                        break
                # possible that it prints too many variations : for ex if we have a snp on the first and the last base of a codon, 
                # while printing the effect of the first snp we aso use the second one.

            else: # size diff !=3k
                print("variation causing a frameshift")
                old_frameshift=frame_shift
                frame_shift=(frame_shift+length_ref-length_alt)%3
                # frameshift=0 -> reading frame recovered. may need to get a base before.
                # frameshift=1 -> frame shift of 1 base to the right
                # frameshift=2 -> frame shift of 2 bases to the right

                if type_var=="insertion":
                    print("insertion of",var[10])
                elif type_var=="deletion":
                    print("deletion of",var[9])
                else:
                    print("substitution of",var[9],"by",var[10])

                len_fragment_before_del=(posVar[0])%3
                len_fragment_before_ins=(posVar[1])%3
                print(len_fragment_before_ins,len_fragment_before_del)

                if frame_shift==0:
                    # print only the local change.
                    len_fragment_after_del=(3-(len_fragment_before_del+length_ref))%3
                    len_fragment_after_ins=(3-(len_fragment_before_ins+length_alt))%3
                    total_ins=sequence_target[posVar[1]-len_fragment_before_ins:posVar[1]+length_alt+len_fragment_after_ins]
                    total_del=cds.sequence[posVar[0]-len_fragment_before_del:posVar[0]+length_ref+len_fragment_after_del]
                    print("recovery of the original reading frame")
                    stop=print_variation_change(total_del,total_ins)
                    if stop:
                        break

                else:
                    # print changes from local var to next var. at the next var, we will see if the reading frame is recovered.
                    print("creating frame shift of",frame_shift,"base(s) to the right.")
                    if old_frameshift==0:
                        print("loss of the original reading frame")
                    if index==len(cds_var[cds_id])-1: # it is the last variation. translate until the end of the cds.
                        total_total_del=cds.sequence[posVar[0]-len_fragment_before_del:]
                        total_total_ins=sequence_target[posVar[1]-len_fragment_before_ins:]
                        stop=print_variation_change(total_total_del,total_total_ins)
                        if stop:
                            break
                    else: 
                        nextVar=cds_var[cds_id][index+1]
                        posNextVar=[int(nextVar[12]),int(nextVar[13])]

                        if nextVar[8]=="insertion":
                            length_ref_nextvar=0
                        else:
                            length_ref_nextvar:len(nextVar[9])
                        if nextVar[8]=="deletion":
                            length_alt_nextvar=0
                        else:
                            length_alt_nextvar=len(nextVar[10])

                        len_fragment_before_del_nextvar=(posNextVar[0])%3
                        len_fragment_before_ins_nextvar=(posNextVar[1])%3
                        total_total_del=cds.sequence[posVar[0]-len_fragment_before_del:posNextVar[0]-len_fragment_before_del_nextvar]
                        total_total_ins=sequence_target[posVar[1]-len_fragment_before_ins:posNextVar[1]-len_fragment_before_ins_nextvar]
                        stop=print_variation_change(total_total_del,total_total_ins)
                        if stop:
                            break

        print("\n")