import csv
import itertools

from uta.exceptions import *


class SeqGeneParser(object):

    """parse mapping data as from ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/current/initial_release/seq_gene.md.gz"""

    def __init__(self, fh, filter=None):
        self._fh = fh
        self._filter = filter if filter else lambda r: True
        header = next(self._fh).rstrip()
        if header != "#tax_id	chromosome	chr_start	chr_stop	chr_orient	contig	ctg_start	ctg_stop	ctg_orient	feature_name	feature_id	feature_type	group_label	transcript	evidence_code":
            raise UTAError("""file doesn't contain expected header; got:\n{header}""".format(
                header=header))
        fields = header.replace("#", "").split("\t")
        self._csvreader = csv.DictReader(
            self._fh, fieldnames=fields, delimiter="\t")

    def __iter__(self):
        return self

    def next(self):
        for r in self._csvreader:
            if self._filter(r):
                return r
        raise StopIteration


# The following code doesn"t work and I don"t know why.
# class SeqGeneBlockParser(object):
##     """parse mapping data as from ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/current/initial_release/seq_gene.md.gz"""
# def __init__(self,fh,filter=None):
##         self._sgparser = SeqGeneParser(fh,filter)
##
# def __iter__(self):
# return self
##
# def next(self):
##         slurp = list(self._sgparser)
##         slurp.sort(key = lambda r: (r["transcript"],r["group_label"],r["chr_start"],r["chr_stop"]))
##         iter = itertools.groupby(slurp, key = lambda r: (r["transcript"],r["group_label"]))
##         import IPython; IPython.embed()
# for k,i in iter:
# return k,i
##         raise StopIteration


if __name__ == "__main__":
    import gzip
    import prettytable
    import IPython
    import sys
    fh = gzip.open(sys.argv[1])
    nm_filter = lambda r: r["transcript"].startswith("NM_")
    sgparser = SeqGeneParser(fh, filter=nm_filter)
    slurp = list(sgparser)
    slurp.sort(key=lambda r: (
        r["transcript"], r["group_label"], r["chr_start"], r["chr_stop"]))
    iter = itertools.groupby(
        slurp, key=lambda r: (r["transcript"], r["group_label"]))
    for k, i in iter:
        print(k, len(list(i)))

# <LICENSE>
# Copyright 2014 UTA Contributors (https://bitbucket.org/biocommons/uta)
##
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
##
# http://www.apache.org/licenses/LICENSE-2.0
##
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# </LICENSE>

fee0aba4bc8f1b0c25863c0186dc3900d099bd39
<mask token>


class SeqGeneParser(object):
    <mask token>

    def __init__(self, fh, filter=None):
        self._fh = fh
        self._filter = filter if filter else lambda r: True
        header = next(self._fh).rstrip()
        if (header !=
            '#tax_id\tchromosome\tchr_start\tchr_stop\tchr_orient\tcontig\tctg_start\tctg_stop\tctg_orient\tfeature_name\tfeature_id\tfeature_type\tgroup_label\ttranscript\tevidence_code'
            ):
            raise UTAError(
                "file doesn't contain expected header; got:\n{header}".
                format(header=header))
        fields = header.replace('#', '').split('\t')
        self._csvreader = csv.DictReader(self._fh, fieldnames=fields,
            delimiter='\t')
    <mask token>

    def next(self):
        for r in self._csvreader:
            if self._filter(r):
                return r
        raise StopIteration


<mask token>

<mask token>


class SeqGeneParser(object):
    <mask token>

    def __init__(self, fh, filter=None):
        self._fh = fh
        self._filter = filter if filter else lambda r: True
        header = next(self._fh).rstrip()
        if (header !=
            '#tax_id\tchromosome\tchr_start\tchr_stop\tchr_orient\tcontig\tctg_start\tctg_stop\tctg_orient\tfeature_name\tfeature_id\tfeature_type\tgroup_label\ttranscript\tevidence_code'
            ):
            raise UTAError(
                "file doesn't contain expected header; got:\n{header}".
                format(header=header))
        fields = header.replace('#', '').split('\t')
        self._csvreader = csv.DictReader(self._fh, fieldnames=fields,
            delimiter='\t')

    def __iter__(self):
        return self

    def next(self):
        for r in self._csvreader:
            if self._filter(r):
                return r
        raise StopIteration


<mask token>

<mask token>


class SeqGeneParser(object):
    """parse mapping data as from ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/current/initial_release/seq_gene.md.gz"""

    def __init__(self, fh, filter=None):
        self._fh = fh
        self._filter = filter if filter else lambda r: True
        header = next(self._fh).rstrip()
        if (header !=
            '#tax_id\tchromosome\tchr_start\tchr_stop\tchr_orient\tcontig\tctg_start\tctg_stop\tctg_orient\tfeature_name\tfeature_id\tfeature_type\tgroup_label\ttranscript\tevidence_code'
            ):
            raise UTAError(
                "file doesn't contain expected header; got:\n{header}".
                format(header=header))
        fields = header.replace('#', '').split('\t')
        self._csvreader = csv.DictReader(self._fh, fieldnames=fields,
            delimiter='\t')

    def __iter__(self):
        return self

    def next(self):
        for r in self._csvreader:
            if self._filter(r):
                return r
        raise StopIteration


if __name__ == '__main__':
    import gzip
    import prettytable
    import IPython
    import sys
    fh = gzip.open(sys.argv[1])
    nm_filter = lambda r: r['transcript'].startswith('NM_')
    sgparser = SeqGeneParser(fh, filter=nm_filter)
    slurp = list(sgparser)
    slurp.sort(key=lambda r: (r['transcript'], r['group_label'], r[
        'chr_start'], r['chr_stop']))
    iter = itertools.groupby(slurp, key=lambda r: (r['transcript'], r[
        'group_label']))
    for k, i in iter:
        print(k, len(list(i)))

import csv
import itertools
from uta.exceptions import *


class SeqGeneParser(object):
    """parse mapping data as from ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/current/initial_release/seq_gene.md.gz"""

    def __init__(self, fh, filter=None):
        self._fh = fh
        self._filter = filter if filter else lambda r: True
        header = next(self._fh).rstrip()
        if (header !=
            '#tax_id\tchromosome\tchr_start\tchr_stop\tchr_orient\tcontig\tctg_start\tctg_stop\tctg_orient\tfeature_name\tfeature_id\tfeature_type\tgroup_label\ttranscript\tevidence_code'
            ):
            raise UTAError(
                "file doesn't contain expected header; got:\n{header}".
                format(header=header))
        fields = header.replace('#', '').split('\t')
        self._csvreader = csv.DictReader(self._fh, fieldnames=fields,
            delimiter='\t')

    def __iter__(self):
        return self

    def next(self):
        for r in self._csvreader:
            if self._filter(r):
                return r
        raise StopIteration


if __name__ == '__main__':
    import gzip
    import prettytable
    import IPython
    import sys
    fh = gzip.open(sys.argv[1])
    nm_filter = lambda r: r['transcript'].startswith('NM_')
    sgparser = SeqGeneParser(fh, filter=nm_filter)
    slurp = list(sgparser)
    slurp.sort(key=lambda r: (r['transcript'], r['group_label'], r[
        'chr_start'], r['chr_stop']))
    iter = itertools.groupby(slurp, key=lambda r: (r['transcript'], r[
        'group_label']))
    for k, i in iter:
        print(k, len(list(i)))

import csv
import itertools

from uta.exceptions import *


class SeqGeneParser(object):

    """parse mapping data as from ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/current/initial_release/seq_gene.md.gz"""

    def __init__(self, fh, filter=None):
        self._fh = fh
        self._filter = filter if filter else lambda r: True
        header = next(self._fh).rstrip()
        if header != "#tax_id	chromosome	chr_start	chr_stop	chr_orient	contig	ctg_start	ctg_stop	ctg_orient	feature_name	feature_id	feature_type	group_label	transcript	evidence_code":
            raise UTAError("""file doesn't contain expected header; got:\n{header}""".format(
                header=header))
        fields = header.replace("#", "").split("\t")
        self._csvreader = csv.DictReader(
            self._fh, fieldnames=fields, delimiter="\t")

    def __iter__(self):
        return self

    def next(self):
        for r in self._csvreader:
            if self._filter(r):
                return r
        raise StopIteration


# The following code doesn"t work and I don"t know why.
# class SeqGeneBlockParser(object):
##     """parse mapping data as from ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/current/initial_release/seq_gene.md.gz"""
# def __init__(self,fh,filter=None):
##         self._sgparser = SeqGeneParser(fh,filter)
##
# def __iter__(self):
# return self
##
# def next(self):
##         slurp = list(self._sgparser)
##         slurp.sort(key = lambda r: (r["transcript"],r["group_label"],r["chr_start"],r["chr_stop"]))
##         iter = itertools.groupby(slurp, key = lambda r: (r["transcript"],r["group_label"]))
##         import IPython; IPython.embed()
# for k,i in iter:
# return k,i
##         raise StopIteration


if __name__ == "__main__":
    import gzip
    import prettytable
    import IPython
    import sys
    fh = gzip.open(sys.argv[1])
    nm_filter = lambda r: r["transcript"].startswith("NM_")
    sgparser = SeqGeneParser(fh, filter=nm_filter)
    slurp = list(sgparser)
    slurp.sort(key=lambda r: (
        r["transcript"], r["group_label"], r["chr_start"], r["chr_stop"]))
    iter = itertools.groupby(
        slurp, key=lambda r: (r["transcript"], r["group_label"]))
    for k, i in iter:
        print(k, len(list(i)))

# <LICENSE>
# Copyright 2014 UTA Contributors (https://bitbucket.org/biocommons/uta)
##
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
##
# http://www.apache.org/licenses/LICENSE-2.0
##
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# </LICENSE>
