from __future__ import absolute_import

from nose.tools import eq_, with_setup

from .data import (
    custom_mouse_genome_grcm38_subset,
    setup_init_custom_mouse_genome
)

@with_setup(setup=setup_init_custom_mouse_genome)
def test_mouse_ENSMUSG00000017167():
    """
    GTF cropped from ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/
    Mus_musculus.GRCm38.81.gtf.gz via:
    grep "ENSMUSG00000017167" Mus_musculus.GRCm38.81.gtf

    Transcript FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/
    fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz via:
    grep "ENSMUSG00000017167" Mus_musculus.GRCm38.cdna.all.fa -A 50

    ncRNA FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/
    fasta/mus_musculus/cdna/Mus_musculus.GRCm38.ncrna.fa.gz via:
    grep "ENSMUSG00000088969" Mus_musculus.GRCm38.ncrna.fa -A 2

    Protein FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/fasta/
    mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz via:
    grep "ENSMUSG00000017167" Mus_musculus.GRCm38.pep.all.fa -A 50

    Tested against:
    http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000017167
    """
    genes_cntnap1 = custom_mouse_genome_grcm38_subset.genes_by_name("Cntnap1")
    eq_(len(genes_cntnap1), 1)
    gene_cntnap1 = genes_cntnap1[0]
    transcripts_cntnap1 = gene_cntnap1.transcripts
    eq_(len(transcripts_cntnap1), 2)
    transcripts_coding_cntnap1 = [
        transcript
        for transcript in transcripts_cntnap1
        if transcript.biotype == "protein_coding"
    ]
    eq_(len(transcripts_coding_cntnap1), 1)
    transcript_cntnap1 = transcripts_coding_cntnap1[0]
    eq_(transcript_cntnap1.sequence[:120],
        ("GAGAGAAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA"
         "GAGAGAGAGAGATTGGGGGTAGGAGAGAGGGAAGGGTGGATAAGGACGGAAAAAAGCTTT"))
    eq_(transcript_cntnap1.protein_sequence[:120],
        ("MMSLRLFSILLATVVSGAWGWGYYGCNEELVGPLYARSLGASSYYGLFTTARFARLHGIS"
         "GWSPRIGDPNPWLQIDLMKKHRIRAVATQGAFNSWDWVTRYMLLYGDRVDSWTPFYQKGH"))
