def read_precursor(precursor, sps=None): def guess_database(args):
def _guess_database_file(gff, database=None):
def get_primary_transcript(database):
def read_gtf_to_mirna(gtf):
def read_gtf_chr2mirna(gtf):  # read from read_gtf_to_precursor
def read_gtf_chr2mirna2(gtf):  # to remove
def read_gtf_to_precursor(gtf):
def _parse_db_mir_chrom(db_mir, db, id_dict):
def _parse_db_mir(db_mir, db, id_dict):
def _parse_db_mir_genomic(db_mir, db, id_dict):
def read_gtf_to_precursor_mirgenedb(gtf, format="precursor"):
def read_gtf_to_precursor_mirbase(gtf, format="precursor"):
def liftover_genomic_precursor(read, genome, hairpin, expected=None): class feature:
    """"Class with alignment information."""

    def __init__(self, line, sep="="):
        # if isinstance(line, basestring) # str in python 3
        if isinstance(line, dict):
            line = self.create_line(line, sep)
        self.line = line
        self.attributes = {}
        self.columns = {}
        self.read_gff_line()
        self.reserved_attributes = gff_versions.ATTRv['1.1']

    def guess_format(self):
        return "=" if self.line.find("Name=") > -1 else " "

    def create_line(self, fields, sep):
        """
        Create GFF/GTF line from dictionary with fields
        """
        # TODO: need unit test. Check all exists.
        fields["attrb"] = ("Read {seq_name}; UID {idseq}; Name {name};"
                           "Parent {parent}; "
                           "Variant {variant}; Cigar {cigar};"
                           "Expression {counts}; "
                           "Filter {filter}; Hits {hits};").format(**fields)

        line = ("{chrom}\t{database}\t{source}\t{start}\t{end}"
                "\t{score}\t{strand}\t.\t{attrb}").format(**fields)
        return line

    def paste_columns(self, sep=None):
        """
        Create GFF/GTF line from read_gff_line
        """
        sep = self.guess_format()
        attributes = "%s;" % "; ".join(
            "%s%s%s" % (a, sep, self.attributes[a]) for a in self.attributes)
        return "\t".join([self.columns['chrom'], self.columns['source'],
                          self.columns['type'],
                          self.columns['start'], self.columns['end'],
                          self.columns['score'],
                          self.columns['strand'], self.columns['ext'],
                          attributes])

    def read_attributes(self, gff_attrb, sep=" "):
        """
        Read GFF/GTF attributes and return dictionary with fields
        """
        sep = self.guess_format()
        gff_dict = OrderedDict()
        for gff_item in gff_attrb.split(";"):
            item_pair = gff_item.strip().split(sep)
            if len(item_pair) > 1:
                gff_dict[item_pair[0].strip()] = item_pair[1].strip()
        self.attributes = gff_dict

    def read_gff_line(self):
        """
        Read GFF/GTF line and return dictionary with fields
        """
        line = self.line
        if line.startswith("#"):
            return line
        cols = line.strip().split("\t")
        if len(cols) != 9:
            raise ValueError("Line has less than 9 elements: %s" % line)
        self.read_attributes(cols[8])
        fields = {'chrom': cols[0],
                  'source': cols[1],
                  'type': cols[2],
                  'start': cols[3],
                  'end': cols[4],
                  'score': cols[5],
                  'strand': cols[6],
                  'ext': cols[7]}
        self.columns = fields def read_samples(fn):
    """Read samples from the header of a GFF file.

    Args:
        *fn(str)*: GFF file to read.

    Returns:
        *(list)*: character list with sample names.
    """
    with open(fn) as inh:
        for line in inh:
            if line.startswith("## COLDATA"):
                return line.strip().split(": ")[1].strip().split(",")
    raise ValueError("%s doesn't contain COLDATA header." % fn) def get_mature_sequence(precursor, mature, exact=False, nt = 5):
    """
    From precursor and mature positions
       get mature sequence with +/- 4 flanking nts.

    Args:
       *precursor(str)*: long sequence.

       *mature(list)*: [start, end].

       *exact(boolean)*: not add 4+/- flanking nts.

       *nt(int)*: number of nts to get.

    Returns:
        *(str)*: mature sequence.
    """
    p = "%s%s" % ("".join(["N"]*nt), precursor)
    s = mature[0] + nt
    e = mature[1] + nt
    if exact:
        return p[s:e + 1]
    return p[s - (nt - 1) :e + nt] def align_from_variants(sequence, mature, variants):
    """
    Giving the sequence read,
       the mature from get_mature_sequence,
       and the variant GFF annotation:
       get a list of substitutions

    Args:
        *sequence(str)*: read sequence.

        *mature(str)*: mature sequence from
            *mirtop.mirna.realing.get_mature_sequence()*.

        *variants(str)*: string from Variant attribute in GFF file.

    Returns:
        *snp(list)*: [[pos, target, reference]]
    """
    init_log = "iso:%s -> %s\nref:%s" % (sequence, variants, mature)
    snps = []
    k = [v.split(":")[0] for v in variants.split(",") if v.find(":") > -1]
    v = [int(v.split(":")[1]) for v in variants.split(",") if v.find(":") > -1]
    var_dict = dict(zip(k, v))
    logger.debug("realign::align_from_variants::sequence %s" % sequence)
    logger.debug("realign::align_from_variants::mature %s" % mature)
    logger.debug("realign::align_from_variants::variants %s" % variants)
    snp = ["iso_snv" for v in variants.split(",") if v.find("snv") > -1]
    fix_5p = 7
    if "iso_5p" in k:
        fix_5p = 7 + var_dict["iso_5p"]
    mature = mature[fix_5p:]
    if "iso_add3p" in k:
        sequence = sequence[:-1 * var_dict["iso_add3p"]]
    if "iso_3p" in k:
        shift = 7 + (-1 * var_dict["iso_3p"])
        if shift != 0:
            mature = mature[:-(shift)]
    else:
        mature = mature[:-7]
    logger.debug("realign::align_from_variants::snp %s" % snp)
    logger.debug("realign::align_from_variants::sequence %s" % sequence)
    logger.debug("realign::align_from_variants::mature %s" % mature)
    if len(sequence) != len(mature):  # in case of indels, align again
        a = align(sequence, mature)
        sequence = a[0]
        mature = a[1]

    if len(sequence) > len(mature):
        logger.warning("Invalid isomiR definition:\n%s\niso:%s\nref:%s" % (init_log, sequence, mature))
        return "Invalid"

    for p in range(0, len(sequence)):
        if sequence[p] != mature[p]:
            if mature[p] == "N":
                continue
            value = ""
            pos = p + 1
            value = "iso_snv"
            logger.debug("realign::align_from_variants::value %s at %s" % (value, pos))
            if value in snp:
                snps.append([pos, sequence[p], mature[p]])
    logger.debug("realign::align_from_variants::snps %s" % snps)
    return snps def read_id(idu):
    """
    Read a unique identifier for the sequence and
    convert it to the nucleotides,
    replacing an unique code for 5 nts.

    It uses the code from *mirtop.mirna.keys()*.

    Inspired by MINTplate: https://cm.jefferson.edu/MINTbase
    https://github.com/TJU-CMC-Org/MINTmap/tree/master/MINTplates

    Args:
        *idu(str)*: unique identifier for the sequence.

    Returns:
        *seq(str)*: nucleotides sequences.
    """
    try:
        seq = convert(idu, False, 'iso')
    except KeyError:
        logger.error("UID is not valid " + idu)
        return False

    return seq def variant_to_5p(hairpin, pos, variant):
    """
    From a sequence and a start position get the nts
       +/- indicated by iso_5p. Pos option is 0-base-index

    Args:
       *hairpin(str)*: long sequence:
            >>> AAATTTT

       *position(int)*: >>> 3

       *variant(int)*: number of nts involved in the variant:
            >>> -1
    Returns:
       *(str)*: nucleotide involved in the variant:
            >>> T
    """
    pos = pos[0]
    iso_t5 = [v for v in variant.split(",") if v.startswith("iso_5p")]
    if iso_t5:
        t5 = int(iso_t5[0].split(":")[-1][-1])
        direction_t5 = int(iso_t5[0].split(":")[-1]) * -1
        if direction_t5 > 0:
            return hairpin[pos - t5:pos]
        elif direction_t5 < 0:
            return hairpin[pos:pos + t5].lower()
    return "0" def variant_to_3p(hairpin, pos, variant):
    """
    From a sequence and a start position get the nts
       +/- indicated by iso_3p. Pos option is 0-base-index

    Args:
       *hairpin(str)*: long sequence:
            >>> AAATTTT

       *position(int)*: >>> 3

       *variant(int)*: number of nts involved in the variant:
            >>> -1
    Returns:
       *(str)*: nucleotide involved in the variant:
            >>> A
    """
    pos = pos[1]
    iso_t3 = [v for v in variant.split(",") if v.startswith("iso_3p")]
    if iso_t3:
        t3 = int(iso_t3[0].split(":")[-1][-1])
        direction_t3 = int(iso_t3[0].split(":")[-1])
        if direction_t3 > 0:
            return hairpin[pos + 1:pos + t3 + 1]
        elif direction_t3 < 0:
            return hairpin[pos - t3 + 1:pos + 1].lower()
    return "0" def variant_to_add(read, variant):
    """
    From a sequence and a start position get the nts
       +/- indicated by iso_3p. Pos option is 0-base-index

    Args:
       *hairpin(str)*: long sequence:
            >>> AAATTTT

       *position(int)*: >>> 3

       *variant(int)*: number of nts involved in the variant:
            >>> 2
    Returns:
       *(str)*: nucleotide involved in the variant:
            >>> TT
    """
    add = [v for v in variant.split(",") if v.startswith("iso_add")]
    if add:
        add = int(add[0].split(":")[-1][-1]) * -1
        return read[add:]
    return "0"
import os
import mirtop.libs.logger as mylog
from mirtop.mirna import fasta, mapper
from mirtop.gff.classgff import feature
from mirtop.gff.header import read_samples
from mirtop.mirna.realign import get_mature_sequence, align_from_variants
from mirtop.mirna.realign import read_id, variant_to_5p, \
                                 variant_to_3p, variant_to_add
""" Read GFF files and output isomiRs compatible format"""
from __future__ import print_function



logger = mylog.getLogger(__name__)


def convert(args):
    """
    Main function to convert from GFF3 to isomiRs Bioc Package.

    Args:
      *args*: supported options for this sub-command.
        See *mirtop.libs.parse.add_subparser_export()*.
    """
    precursors = fasta.read_precursor(args.hairpin, args.sps)
    matures = mapper.read_gtf_to_precursor(args.gtf)
    for fn in args.files:
        logger.info("Reading %s" % fn)
        _read_file(fn, precursors, matures, args.out)


def _read_file(fn, precursors, matures, out_dir):

    samples = read_samples(fn)