#!/usr/bin/env python
import time
import sys
import argparse

from Fred2.Core import Protein, Peptide, Allele, MutationSyntax, Variant
from Fred2.Core.Variant import VariationType
from Fred2.IO import read_lines, MartsAdapter, read_annovar_exonic
from Fred2.EpitopePrediction import EpitopePredictorFactory
from Fred2.Core import generate_peptides_from_proteins, generate_peptides_from_variants, generate_transcripts_from_variants, generate_proteins_from_transcripts
from Fred2.IO.ADBAdapter import EIdentifierTypes, EAdapterFields
from vcf_reader import read_vcf


MARTDBURL = {"GRCH37": "http://grch37.ensembl.org/biomart/martservice?query=",
                "GRCH38": "http://www.ensembl.org/biomart/martservice?query="} # is corrently set to GRCh38

def read_variant_effect_predictor(file, gene_filter=None):
    """
    Reads a VCF (v4.1) file generatede by variant effect predictor and generates variant objects
    :param str file: Path to vcf file
    :param list gene_filter: List of proteins (in HGNC) of inerrest. Variants are filter according to this list
    :return: list(Variant) - a list of Fred2.Core.Variant objects
    """
    vars = []
    def get_type(ref, alt):
        """
            returns the variant type
        """
        if len(ref)==1 and len(alt)==1:
            return VariationType.SNP
        if len(ref)>0 and len(alt)==0:
            if len(ref)%3 == 0:
                return VariationType.DEL
            else:
                return VariationType.FSDEL
        if len(ref) == 0 and len(alt)>0:
            if len(alt)% 3 == 0:
                return VariationType.INS
            else:
                return VariationType.FSINS
        return VariationType.UNKNOWN

    coding_types = set(["3_prime_UTR_variant", "5_prime_UTR_variant", "start_lost", "stop_gained",
        "frameshift_variant", "start_lost", "inframe_insertion", "inframe_deletion", "missense_variant",
        "protein_altering_variant", "splice_region_variant", "incomplete_terminal_codon_variant", "stop_retained_variant",
        "synonymous_variant", "coding_sequence_variant"])

    with open(file, "r") as f:
        for i,l in enumerate(f):

            #skip comments
            if l.startswith("#") or l.strip() == "":
                continue

            chrom, gene_pos,var_id,ref,alt,_,filter_flag,info= l.strip().split("\t")[:8]
            coding = {}
            isSynonymous = False

            for co in info.split(","):
                #Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|TSL|APPRIS|SIFT|PolyPhen|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE">
                _,var_type,_,gene,_,transcript_type,transcript_id,_,_,_,_,_,_,transcript_pos,prot_pos,aa_mutation = co.strip().split("|")[:16]
                HGNC_ID=co.strip().split("|")[22]

                #pass every other feature type except Transcript (RegulatoryFeature, MotifFeature.)
                #pass genes that are uninterresting for us
                if transcript_type != "Transcript" or (HGNC_ID not in gene_filter and gene_filter):
                    continue

                #pass all intronic and other mutations that do not directly influence the protein sequence
                if any(t in coding_types for t in var_type.split("&")):
                    #generate mutation syntax

                    #positioning in Fred2 is 0-based!!!
                    if transcript_pos != "":
                        coding[transcript_id] = MutationSyntax(transcript_id, int(transcript_pos)-1,
                            -1 if prot_pos  == "" else int(prot_pos)-1, co, "", geneID=HGNC_ID)

                #is variant synonymous?
                isSynonymous = any(t == "synonymous_variant" for t in var_type.split("&"))
            if coding:
                vars.append(Variant(var_id, get_type(ref, alt), chrom, int(gene_pos), ref.upper(), alt.upper(), coding, False, isSynonymous))
    return vars


def main():

    model = argparse.ArgumentParser(description='Neoepitope protein fasta generation from variant vcf')

    model.add_argument(
        '-v', '--vcf',
        type=str,
        default=None,
        help='Path to the vcf input file'
        )

    model.add_argument(
        '-t', '--type',
        type=str,
        choices=["VEP", "ANNOVAR", "SNPEFF"],
        default="VEP",
        help='Type of annotation tool used (Variant Effect Predictor, ANNOVAR exonic gene annotation, SnpEff)'
        )

    model.add_argument(
        '-f', '--fasta_ref',
        type=str,
        default=None,
        help='Path to the fasta input file'
        )

    model.add_argument(
        '-p','--proteins',
        type=str,
        default=None,
        help='Path to the protein ID input file (in HGNC-ID)'
        )

    model.add_argument(
        '-r' ,'--reference',
        type=str,
        default='GRCh38',
        help='The reference genome used for varinat annotation and calling.'
        )

    model.add_argument(
        '-fINDEL' ,'--filterINDEL',
        action="store_true",
        help='Filter insertions and deletions (including frameshifts)'
        )

    model.add_argument(
        '-fFS' ,'--filterFSINDEL',
        action="store_true",
        help='Filter frameshift INDELs'
        )

    model.add_argument(
        '-fSNP' ,'--filterSNP',
        action="store_true",
        help='Filter SNPs'
        )

    model.add_argument(
        '-o','--output',
        type=str,
        required=True,
        help='Path to the output file'
        )


    args = model.parse_args()

    martDB = MartsAdapter(biomart=MARTDBURL[args.reference.upper()])


    if args.vcf is None:
        sys.stderr.write("At least a vcf file or a protein id file has to be provided.\n")
        return -1

    # if vcf file is given: generate variants and filter them if HGNC IDs ar given
    if args.vcf is not None:
        protein_ids = []
        if args.proteins is not None:
            with open(args.proteins, "r") as f:
                for l in f:
                    l = l.strip()
                    if l != "":
                        protein_ids.append(l)

        if args.type == "VEP":
            variants = read_variant_effect_predictor(args.vcf, gene_filter=protein_ids)

        elif args.type == "SNPEFF":
            variants = read_vcf(args.vcf)[0]

        else:
            variants = read_annovar_exonic(args.vcf, gene_filter=protein_ids)


        if args.filterSNP:
            variants = filter(lambda x: x.type != VariationType.SNP, variants)

        if args.filterINDEL:
            variants = filter(lambda x: x.type not in [VariationType.INS, VariationType.DEL, VariationType.FSDEL, VariationType.FSINS], variants)

        if args.filterFSINDEL:
            variants = filter(lambda x: x.type not in [VariationType.FSDEL, VariationType.FSINS], variants)

        if not variants:
            sys.stderr.write("No variants left after filtering. Please refine your filtering criteria.\n")
            return -1

        #generate transcripts
        transcripts = generate_transcripts_from_variants(variants, martDB, EIdentifierTypes.ENSEMBL)

        #generate proteins
        proteins = generate_proteins_from_transcripts(transcripts)

        print(proteins)

        #write fasta file
        with open(args.output.replace('.fasta','_vcf.fasta'), "w") as f:
            for p in proteins:
                f.write('>' + str(p.transcript_id) + '|' + str(p.vars) + '_var_' + '\n')
                f.write(str(p)+ '\n')


        #concatenate fasta file with fasta reference
        op=open(args.output.replace('.fasta','_vcf.fasta'))
        opr1=op.read()
        op.close()

        op=open(args.fasta_ref)
        opr2=op.read()
        op.close()

        concat=opr1+opr2

        op=open(args.output,'w')
        op.write(concat)
        op.close()

    else:
        sys.stderr.write("At least a vcf file or a protein id file has to be provided.\n")
        return -1

    return 0



if __name__ == "__main__":
    sys.exit(main())

