def setUp(self):
# Forward
self.fwd = {
"exon_1": Exon(10, 30, "+", "chr1"),
"exon_2": Exon(40, 70, "+", "chr1"),
"exon_3": Exon(80, 100, "+", "chr1"),
"intron_1": Intron(31, 39, "+", "chr1"),
"intron_2": Intron(71, 79, "+", "chr1")
}
self.fwd["transcript"] = Transcript(10,
100,
"+",
"chr1",
children=[
self.fwd["exon_1"],
self.fwd["exon_3"],
self.fwd["exon_2"]
])
# Reverse
self.rvs = {
"exon_1": Exon(10, 30, "-", "chr1"),
"exon_2": Exon(40, 70, "-", "chr1"),
"exon_3": Exon(80, 100, "-", "chr1"),
"intron_1": Intron(31, 39, "-", "chr1"),
"intron_2": Intron(71, 79, "-", "chr1")
}
self.rvs["transcript"] = Transcript(reference="chr1",
children=[
self.rvs["exon_1"],
self.rvs["exon_3"],
self.rvs["exon_2"]
])
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_fasta_idx = os.path.join(tmp_folder, unique_id + ".fasta.fai")
self.tmp_fasta = os.path.join(tmp_folder, unique_id + ".fasta")
# Create sequence file
content_fasta = """>one
ATGCATGCATGCATGCATGCATGCATGCAT
GCATGCATGCATGCATGCATGCATGCATGC
ATGCAT
>two another chromosome
ATGCATGCATGCAT
GCATGCATGCATGC"""
with open(self.tmp_fasta, "w") as FH_out:
FH_out.write(content_fasta)
# Proteins
# 1 3 5 7 9 11 14 16 19 21 30 33 36 39 41 44 47 50
# ATGCATGCAT GCATG CATGC ATGCATGCA TGCATGCATGC ATGCATGCATGCATGCATGC
# ..... ***** *******.... ......
# prot_1 12345 6789 11
tr_1 = Transcript(None,
None,
"+",
"one",
children=[
Exon(10, 20, "+", "one"),
Exon(30, 40, "+", "one"),
Exon(45, 50, "+", "one")
])
self.prot_1 = Protein(16, 36, "+", "one", transcript=tr_1)
tr_2 = Transcript(None,
None,
"-",
"one",
children=[
Exon(10, 20, "-", "one"),
Exon(30, 40, "-", "one"),
Exon(45, 50, "-", "one")
])
self.prot_2 = Protein(16, 36, "-", "one", transcript=tr_2)
# Create index
content_fasta_idx = """one 66 5 30 31
two 28 98 14 15"""
with open(self.tmp_fasta_idx, "w") as FH_out:
FH_out.write(content_fasta_idx)
def testSetProteins(self):
# By init
protein_1 = Protein(10, 30, "+", "chr1", "p1")
protein_2 = Protein(32, 50, "+", "chr1", "p2")
transcript_1 = Transcript(name="tr1", proteins=[protein_1, protein_2])
self.assertEqual([prot.name for prot in transcript_1.proteins],
[protein_1.name, protein_2.name])
self.assertEqual(
[protein_1.transcript.name, protein_2.transcript.name],
[transcript_1.name, transcript_1.name])
# By method
protein_1 = Protein(10, 30, "+", "chr1", "p1")
protein_2 = Protein(32, 50, "+", "chr1", "p2")
transcript_1 = Transcript(name="tr1")
transcript_1.proteins = [protein_1, protein_2]
self.assertEqual([prot.name for prot in transcript_1.proteins],
[protein_1.name, protein_2.name])
self.assertEqual(
[protein_1.transcript.name, protein_2.transcript.name],
[transcript_1.name, transcript_1.name])
# Replace proteins
protein_1 = Protein(10, 30, "+", "chr1", "p1")
protein_2 = Protein(32, 50, "+", "chr1", "p2")
protein_3 = Protein(54, 70, "+", "chr1", "p3")
transcript_1 = Transcript(name="tr1", proteins=[protein_1, protein_3])
transcript_1.proteins = [protein_2, protein_3]
self.assertIsNone(protein_1.transcript)
self.assertNotIn(protein_1, transcript_1.proteins)
self.assertEqual(protein_2.transcript, transcript_1)
self.assertIn(protein_2, transcript_1.proteins)
self.assertEqual(protein_3.transcript, transcript_1)
self.assertIn(protein_3, transcript_1.proteins)
def testGetPosOnRegion(self):
# Forward
self.assertEqual(self.fwd["transcript"].getPosOnRegion(10), 1)
self.assertEqual(self.fwd["transcript"].getPosOnRegion(20), 11)
self.assertEqual(self.fwd["transcript"].getPosOnRegion(30), 21)
self.assertEqual(self.fwd["transcript"].getPosOnRegion(40), 22)
self.assertEqual(self.fwd["transcript"].getPosOnRegion(80), 53)
# Reverse
self.assertEqual(self.rvs["transcript"].getPosOnRegion(100), 1)
self.assertEqual(self.rvs["transcript"].getPosOnRegion(90), 11)
self.assertEqual(self.rvs["transcript"].getPosOnRegion(80), 21)
self.assertEqual(self.rvs["transcript"].getPosOnRegion(70), 22)
self.assertEqual(self.rvs["transcript"].getPosOnRegion(30), 53)
# Exception out of transcript
with self.assertRaises(Exception):
self.fwd["transcript"].getPosOnRegion(8)
# Exception in intron
with self.assertRaises(Exception):
self.fwd["transcript"].getPosOnRegion(31)
# Exception strand
unstranded_tr = Transcript(10, 30, None, "chr1")
with self.assertRaises(Exception):
unstranded_tr.getPosOnRegion(20)
def addProtein(self):
protein_1 = Protein(10, 30, "+", "chr1", "p1")
protein_2 = Protein(32, 50, "+", "chr1", "p2")
transcript_1 = Transcript(name="tr1")
# Empty
self.assertEqual([elt.name for elt in transcript_1.proteins], [])
# Add protein_1
transcript_1.addProtein(protein_1)
self.assertEqual([elt.name for elt in transcript_1.proteins],
["p1"]) # Check from tr
self.assertEqual(protein_1.transcript, transcript_1) # Check from prot
# Add protein_2
transcript_1.addProtein(protein_2)
self.assertEqual([elt.name for elt in transcript_1.proteins],
["p1", "p2"]) # Check from tr
self.assertEqual(protein_1.transcript, transcript_1) # Check from prot
self.assertEqual(protein_2.transcript, transcript_1) # Check from prot
def getTranscriptAnnot(in_annot, gene_by_tr):
"""
Get genomic model (genes, transcripts and exons) for the selected transcripts.
:param in_annot: Path to the genomic annotations (format: GFF3).
:type in_annot: str
:param gene_by_tr: Gene by selected transcripts.
:type gene_by_tr: dict
:return: The list of selected transcripts.
:rtype: anacore.region.RegionList
"""
tr_by_id = dict()
with GFF3IO(in_annot) as FH_annot:
for record in FH_annot:
if record.type == "mRNA" and "transcript_id" in record.annot:
tr_id = record.annot["transcript_id"]
tr_id = tr_id.split(".")[0] # Remove transcript version
if tr_id in gene_by_tr: # Transcript is in panel
if tr_id not in tr_by_id:
tr_by_id[tr_id] = Transcript(record.start, record.end,
record.strand,
record.seq_id, tr_id, {},
gene_by_tr[tr_id])
if record.type == "exon" and "transcript_id" in record.annot:
tr_id = record.annot["transcript_id"]
tr_id = tr_id.split(".")[0] # Remove transcript version
if tr_id in gene_by_tr: # Transcript is in panel
# Store the exon
tr_by_id[tr_id].addChild(
Exon(record.start, record.end, record.strand,
record.seq_id))
if len(gene_by_tr) != len(tr_by_id):
raise Exception(
"The following transcripts are missing in {}: {}".format(
args.input_annotation,
set(gene_by_tr.keys()).difference(set(tr_by_id.keys()))))
return RegionList(tr_by_id.values())
def delProtein(self):
protein_1 = Protein(10, 30, "+", "chr1", "p1")
protein_2 = Protein(32, 50, "+", "chr1", "p2")
transcript_1 = Transcript(name="tr1", proteins=[protein_1, protein_2])
# Init
self.assertEqual([elt.name for elt in transcript_1.proteins],
["p1", "p2"]) # Check from tr
self.assertEqual(protein_1.transcript, transcript_1) # Check from prot
self.assertEqual(protein_2.transcript, transcript_1) # Check from prot
# Delete protein 2
transcript_1.delProtein(protein_2)
self.assertEqual([elt.name for elt in transcript_1.proteins],
["p1"]) # Check from tr
self.assertEqual(protein_1.transcript, transcript_1) # Check from prot
self.assertEqual(protein_2.transcript, None) # Check from prot
# Delete protein 1
transcript_1.addProtein(protein_1)
self.assertEqual([elt.name for elt in transcript_1.proteins],
[]) # Check from tr
self.assertEqual(protein_1.transcript, None) # Check from prot
self.assertEqual(protein_2.transcript, None) # Check from prot
def testGetTranscriptsAnnot_withoutUTR_oneExon(self):
exon_1 = Exon(91, 150, "+", "chr1", "exon_2")
cds_1 = CDS(91, 150, "+", "chr1", "cds_1")
gene_1 = Gene(10, 350, None, "chr1", "gene_1", {"id": "g_1"})
transcrit_1 = Transcript(None,
None,
None,
"chr1",
"transcrit_1", {"id": "tr_1"},
parent=gene_1,
children=[exon_1])
protein_1 = Protein(None,
None,
None,
"chr1",
"protein_2",
children=[cds_1],
transcript=transcrit_1)
queries = [
Region(80, 160, None, "chr1", "query_1",
{"desc": "starts before exon_1 ; ends after exon_1."}),
Region(
91, 150, None, "chr1", "query_2",
{"desc": "starts at start of exon_1 ; ends at end of exon_1."
}),
Region(100, 110, None, "chr1", "query_3",
{"desc": "starts in exon_1 ; ends in exon_1."}),
Region(80, 100, None, "chr1", "query_4",
{"desc": "starts before exon_1 ; ends in exon_1."}),
Region(110, 200, None, "chr1", "query_5",
{"desc": "starts in exon_1 ; ends after exon_1."}),
]
# Expected forward 1 exon
expected = {
"query_1": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 1,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 20
},
"query_2": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 1,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 20
},
"query_3": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 4,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 7
},
"query_4": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 1,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 4
},
"query_5": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 7,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 20
},
}
for query_name, query_res in expected.items():
for key, val in {
"SYMBOL": "gene_1",
"Gene": "g_1",
"Feature": "tr_1",
"Feature_type": "Transcript",
"STRAND": "1"
}.items():
query_res[key] = val
# Apply forward strand
for exon in transcrit_1.children:
exon.strand = "+"
for cds in protein_1.children:
cds.strand = "+"
transcrit_1.sortChildren()
protein_1.sortChildren()
# Asert
for curr_query in queries:
annotations = getTranscriptsAnnot(curr_query, [transcrit_1])
self.assertEqual([expected[curr_query.name]], annotations)
# Expected reverse 1 exon
expected = {
"query_1": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 1,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 20
},
"query_2": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 1,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 20
},
"query_3": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 14,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 17
},
"query_4": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 17,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 20
},
"query_5": {
"start_EXON": "1/1",
"start_INTRON": None,
"start_Protein_position": 1,
"end_EXON": "1/1",
"end_INTRON": None,
"end_Protein_position": 14
},
}
for query_name, query_res in expected.items():
for key, val in {
"SYMBOL": "gene_1",
"Gene": "g_1",
"Feature": "tr_1",
"Feature_type": "Transcript",
"STRAND": "-1"
}.items():
query_res[key] = val
# Apply reverse strand
for exon in transcrit_1.children:
exon.strand = "-"
for cds in protein_1.children:
cds.strand = "-"
transcrit_1.sortChildren()
protein_1.sortChildren()
# Asert
for curr_query in queries:
annotations = getTranscriptsAnnot(curr_query, [transcrit_1])
self.assertEqual([expected[curr_query.name]], annotations)
def testGetTranscriptsAnnot_withoutUTR_threeExons(self):
exon_1 = Exon(10, 40, "+", "chr1", "fwd_exon_1")
exon_2 = Exon(91, 150, "+", "chr1", "fwd_exon_2")
exon_3 = Exon(201, 361, "+", "chr1", "fwd_exon_3")
cds_1 = CDS(10, 40, "+", "chr1", "fwd_cds_1")
cds_2 = CDS(91, 150, "+", "chr1", "fwd_cds_2")
cds_3 = CDS(201, 361, "+", "chr1", "fwd_cds_3")
gene_1 = Gene(10, 350, None, "chr1", "gene_1", {"id": "g_1"})
transcrit_1 = Transcript(None,
None,
None,
"chr1",
"transcrit_1", {"id": "tr_1"},
parent=gene_1,
children=[exon_1, exon_2, exon_3])
protein_1 = Protein(None,
None,
None,
"chr1",
"protein_1",
children=[cds_1, cds_2, cds_3],
transcript=transcrit_1)
queries = [
Region(80, 100, None, "chr1", "query_1",
{"desc": "starts before exon_2 ; ends in exon_2."}),
Region(100, 180, None, "chr1", "query_2",
{"desc": "starts in exon_2 ; ends after exon_2."}),
Region(
91, 150, None, "chr1", "query_3", {
"desc":
"starts at the start of exon_2 ; ends at the end of exon_2."
}),
Region(80, 170, None, "chr1", "query_4",
{"desc": "starts before exon_2 ; ends after exon_2."}),
Region(80, 230, None, "chr1", "query_5",
{"desc": "starts before exon_2 ; ends in exon_3."}),
Region(100, 400, None, "chr1", "query_6",
{"desc": "starts in exon_2 ; ends after exon_3."}),
Region(100, 250, None, "chr1", "query_7",
{"desc": "starts in exon_2 ; ends in exon_3."}),
Region(80, 370, None, "chr1", "query_8",
{"desc": "starts before exon_2 ; ends after exon_3."}),
Region(90, 151, None, "chr1", "query_9", {
"desc":
"starts just before exon_2 ; ends just after exon_2."
})
]
# Expected forward 3 exons
expected = {
"query_1": {
"start_EXON": None,
"start_INTRON": "1/2",
"start_Protein_position": 11,
"end_EXON": "2/3",
"end_INTRON": None,
"end_Protein_position": 14
},
"query_2": {
"start_EXON": "2/3",
"start_INTRON": None,
"start_Protein_position": 14,
"end_EXON": None,
"end_INTRON": "2/2",
"end_Protein_position": 31
},
"query_3": {
"start_EXON": "2/3",
"start_INTRON": None,
"start_Protein_position": 11,
"end_EXON": "2/3",
"end_INTRON": None,
"end_Protein_position": 31
},
"query_4": {
"start_EXON": None,
"start_INTRON": "1/2",
"start_Protein_position": 11,
"end_EXON": None,
"end_INTRON": "2/2",
"end_Protein_position": 31
},
"query_5": {
"start_EXON": None,
"start_INTRON": "1/2",
"start_Protein_position": 11,
"end_EXON": "3/3",
"end_INTRON": None,
"end_Protein_position": 41
},
"query_6": {
"start_EXON": "2/3",
"start_INTRON": None,
"start_Protein_position": 14,
"end_EXON": "3/3",
"end_INTRON": None,
"end_Protein_position": 84
},
"query_7": {
"start_EXON": "2/3",
"start_INTRON": None,
"start_Protein_position": 14,
"end_EXON": "3/3",
"end_INTRON": None,
"end_Protein_position": 47
},
"query_8": {
"start_EXON": None,
"start_INTRON": "1/2",
"start_Protein_position": 11,
"end_EXON": "3/3",
"end_INTRON": None,
"end_Protein_position": 84
},
"query_9": {
"start_EXON": None,
"start_INTRON": "1/2",
"start_Protein_position": 11,
"end_EXON": None,
"end_INTRON": "2/2",
"end_Protein_position": 31
},
}
for query_name, query_res in expected.items():
for key, val in {
"SYMBOL": "gene_1",
"Gene": "g_1",
"Feature": "tr_1",
"Feature_type": "Transcript",
"STRAND": "1"
}.items():
query_res[key] = val
# Apply forward strand
for exon in transcrit_1.children:
exon.strand = "+"
for cds in protein_1.children:
cds.strand = "+"
transcrit_1.sortChildren()
protein_1.sortChildren()
# Assert
for curr_query in queries:
annotations = getTranscriptsAnnot(curr_query, [transcrit_1])
self.assertEqual([expected[curr_query.name]], annotations)
# Expected reverse 3 exons
expected = {
"query_1": {
"start_EXON": "2/3",
"start_INTRON": None,
"start_Protein_position": 71,
"end_EXON": None,
"end_INTRON": "2/2",
"end_Protein_position": 74
},
"query_2": {
"start_EXON": None,
"start_INTRON": "1/2",
"start_Protein_position": 54,
"end_EXON": "2/3",
"end_INTRON": None,
"end_Protein_position": 71
},
"query_3": {
"start_EXON": "2/3",
"start_INTRON": None,
"start_Protein_position": 54,
"end_EXON": "2/3",
"end_INTRON": None,
"end_Protein_position": 74
},
"query_4": {
"start_EXON": None,
"start_INTRON": "1/2",
"start_Protein_position": 54,
"end_EXON": None,
"end_INTRON": "2/2",
"end_Protein_position": 74
},
"query_5": {
"start_EXON": "1/3",
"start_INTRON": None,
"start_Protein_position": 44,
"end_EXON": None,
"end_INTRON": "2/2",
"end_Protein_position": 74
},
"query_6": {
"start_EXON": "1/3",
"start_INTRON": None,
"start_Protein_position": 1,
"end_EXON": "2/3",
"end_INTRON": None,
"end_Protein_position": 71
},
"query_7": {
"start_EXON": "1/3",
"start_INTRON": None,
"start_Protein_position": 38,
"end_EXON": "2/3",
"end_INTRON": None,
"end_Protein_position": 71
},
"query_8": {
"start_EXON": "1/3",
"start_INTRON": None,
"start_Protein_position": 1,
"end_EXON": None,
"end_INTRON": "2/2",
"end_Protein_position": 74
},
"query_9": {
"start_EXON": None,
"start_INTRON": "1/2",
"start_Protein_position": 54,
"end_EXON": None,
"end_INTRON": "2/2",
"end_Protein_position": 74
}
}
for query_name, query_res in expected.items():
for key, val in {
"SYMBOL": "gene_1",
"Gene": "g_1",
"Feature": "tr_1",
"Feature_type": "Transcript",
"STRAND": "-1"
}.items():
query_res[key] = val
# Apply reverse strand
for exon in transcrit_1.children:
exon.strand = "-"
for cds in protein_1.children:
cds.strand = "-"
transcrit_1.sortChildren()
protein_1.sortChildren()
# Asert
for curr_query in queries:
annotations = getTranscriptsAnnot(curr_query, [transcrit_1])
self.assertEqual([expected[curr_query.name]], annotations)
def testGetCodonRefPos(self):
tr_1 = Transcript(None,
None,
"+",
"chr1",
children=[
Exon(10, 20, "+", "chr1"),
Exon(30, 40, "+", "chr1"),
Exon(45, 50, "+", "chr1")
])
prot_1 = Protein(16, 36, "+", "chr1", transcript=tr_1)
tr_2 = Transcript(None,
None,
"-",
"chr1",
children=[
Exon(10, 20, "-", "chr1"),
Exon(30, 40, "-", "chr1"),
Exon(45, 50, "-", "chr1")
])
prot_2 = Protein(16, 36, "-", "chr1", transcript=tr_2)
data = [
{
"prot": prot_1,
"aa_pos": 1,
"expected": [16, 17, 18]
},
{
"prot": prot_1,
"aa_pos": 2,
"expected": [19, 20, 30]
},
{
"prot": prot_1,
"aa_pos": 3,
"expected": [31, 32, 33]
},
{
"prot": prot_1,
"aa_pos": 4,
"expected": [34, 35, 36]
},
{
"prot": prot_2,
"aa_pos": 1,
"expected": [36, 35, 34]
},
{
"prot": prot_2,
"aa_pos": 2,
"expected": [33, 32, 31]
},
{
"prot": prot_2,
"aa_pos": 3,
"expected": [30, 20, 19]
},
{
"prot": prot_2,
"aa_pos": 4,
"expected": [18, 17, 16]
},
]
for curr in data:
self.assertEqual(curr["prot"].getCodonRefPos(curr["aa_pos"]),
curr["expected"])
with self.assertRaises(Exception):
self.prot_1.getCodonRefPos(8) # Not in protein
def testGetCDSFromTranscript(self):
res = []
# One exon forward
transcript_1 = Transcript(None,
None,
"+",
"chr1",
children=[Exon(100, 150, "+", "chr1")])
res.append({
"expected": [CDS(100, 150, "+", "chr1")],
"observed":
Protein(100, 150, "+", "chr1",
transcript=transcript_1).getCDSFromTranscript()
})
res.append({
"expected": [CDS(110, 140, "+", "chr1")],
"observed":
Protein(110, 140, "+", "chr1",
transcript=transcript_1).getCDSFromTranscript()
})
res.append({
"expected": [CDS(110, 150, "+", "chr1")],
"observed":
Protein(110, 150, "+", "chr1",
transcript=transcript_1).getCDSFromTranscript()
})
res.append({
"expected": [CDS(100, 140, "+", "chr1")],
"observed":
Protein(100, 140, "+", "chr1",
transcript=transcript_1).getCDSFromTranscript()
})
# Three exons forward
transcript_2 = Transcript(None,
None,
"+",
"chr1",
children=[
Exon(30, 80, "+", "chr1"),
Exon(100, 150, "+", "chr1"),
Exon(170, 200, "+", "chr1")
])
res.append({
"expected": [CDS(100, 150, "+", "chr1")],
"observed":
Protein(100, 150, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(110, 140, "+", "chr1")],
"observed":
Protein(110, 140, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(110, 150, "+", "chr1")],
"observed":
Protein(110, 150, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(100, 140, "+", "chr1")],
"observed":
Protein(100, 140, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(30, 80, "+", "chr1"),
CDS(100, 150, "+", "chr1")],
"observed":
Protein(30, 150, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(60, 80, "+", "chr1"),
CDS(100, 150, "+", "chr1")],
"observed":
Protein(60, 150, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(80, 80, "+", "chr1"),
CDS(100, 150, "+", "chr1")],
"observed":
Protein(80, 150, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [
CDS(80, 80, "+", "chr1"),
CDS(100, 150, "+", "chr1"),
CDS(170, 170, "+", "chr1")
],
"observed":
Protein(80, 170, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected":
[CDS(100, 150, "+", "chr1"),
CDS(170, 200, "+", "chr1")],
"observed":
Protein(100, 200, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected":
[CDS(100, 150, "+", "chr1"),
CDS(170, 190, "+", "chr1")],
"observed":
Protein(100, 190, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected":
[CDS(110, 150, "+", "chr1"),
CDS(170, 200, "+", "chr1")],
"observed":
Protein(110, 200, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected":
[CDS(110, 150, "+", "chr1"),
CDS(170, 190, "+", "chr1")],
"observed":
Protein(110, 190, "+", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
# One exon reverse
transcript_1 = Transcript(None,
None,
"-",
"chr1",
children=[Exon(100, 150, "-", "chr1")])
res.append({
"expected": [CDS(100, 150, "-", "chr1")],
"observed":
Protein(100, 150, "-", "chr1",
transcript=transcript_1).getCDSFromTranscript()
})
res.append({
"expected": [CDS(110, 140, "-", "chr1")],
"observed":
Protein(110, 140, "-", "chr1",
transcript=transcript_1).getCDSFromTranscript()
})
res.append({
"expected": [CDS(110, 150, "-", "chr1")],
"observed":
Protein(110, 150, "-", "chr1",
transcript=transcript_1).getCDSFromTranscript()
})
res.append({
"expected": [CDS(100, 140, "-", "chr1")],
"observed":
Protein(100, 140, "-", "chr1",
transcript=transcript_1).getCDSFromTranscript()
})
# Three exons reverse
transcript_2 = Transcript(None,
None,
"-",
"chr1",
children=[
Exon(170, 200, "-", "chr1"),
Exon(100, 150, "-", "chr1"),
Exon(30, 80, "-", "chr1")
])
res.append({
"expected": [CDS(100, 150, "-", "chr1")],
"observed":
Protein(100, 150, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(110, 140, "-", "chr1")],
"observed":
Protein(110, 140, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(110, 150, "-", "chr1")],
"observed":
Protein(110, 150, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(100, 140, "-", "chr1")],
"observed":
Protein(100, 140, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(100, 150, "-", "chr1"),
CDS(30, 80, "-", "chr1")],
"observed":
Protein(30, 150, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(100, 150, "-", "chr1"),
CDS(60, 80, "-", "chr1")],
"observed":
Protein(60, 150, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [CDS(100, 150, "-", "chr1"),
CDS(80, 80, "-", "chr1")],
"observed":
Protein(80, 150, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected": [
CDS(170, 170, "-", "chr1"),
CDS(100, 150, "-", "chr1"),
CDS(80, 80, "-", "chr1")
],
"observed":
Protein(80, 170, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected":
[CDS(170, 200, "-", "chr1"),
CDS(100, 150, "-", "chr1")],
"observed":
Protein(100, 200, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected":
[CDS(170, 190, "-", "chr1"),
CDS(100, 150, "-", "chr1")],
"observed":
Protein(100, 190, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected":
[CDS(170, 200, "-", "chr1"),
CDS(110, 150, "-", "chr1")],
"observed":
Protein(110, 200, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
res.append({
"expected":
[CDS(170, 190, "-", "chr1"),
CDS(110, 150, "-", "chr1")],
"observed":
Protein(110, 190, "-", "chr1",
transcript=transcript_2).getCDSFromTranscript()
})
# Launch evaluation
for eval_pair in res:
self.assertEqual(
", ".join([
curr_cds.getCoordinatesStr()
for curr_cds in eval_pair["expected"]
]),
", ".join([
curr_cds.getCoordinatesStr()
for curr_cds in eval_pair["observed"]
]),
)
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_ensembl_in_gtf = os.path.join(tmp_folder,
unique_id + "_ensembl_in.gtf")
self.tmp_ensembl_out_gtf = os.path.join(tmp_folder,
unique_id + "_ensembl_out.gtf")
self.tmp_ncbi_in_gtf = os.path.join(tmp_folder,
unique_id + "_ncbi_in.gtf")
self.tmp_ncbi_out_gtf = os.path.join(tmp_folder,
unique_id + "_ncbi_out.gtf")
# Ensembl GTF
self.ensembl_expected = [
Gene(54770583, 54771134, "+", "6", "KRASP1", {
"id": "ENSG00000220635"
}, None, [
Transcript(
54770583, 54771134, "+", "6", "KRASP1-201",
{"id": "ENST00000407852"}, None,
[Exon(54770583, 54771134, "+", "6", "ENST00000407852_e1")])
]),
Gene(
25204789, 25250936, "-", "12", "KRAS",
{"id": "ENSG00000133703"}, None, [
Transcript(
25204789, 25250931, "-", "12", "KRAS-202",
{"id": "ENST00000311936"}, None, [
Exon(25250751, 25250931, "-", "12",
"ENST00000311936_e1"),
Exon(25245274, 25245395, "-", "12",
"ENST00000311936_e2"),
Exon(25227234, 25227412, "-", "12",
"ENST00000311936_e3"),
Exon(25225614, 25225773, "-", "12",
"ENST00000311936_e5"),
Exon(25204789, 25209911, "-", "12",
"ENST00000311936_e6")
], [
Protein(25209798, 25245384, "-", "12", None, None,
None, [
CDS(25245274, 25245384, "-", "12", ""),
CDS(25227234, 25227412, "-", "12", ""),
CDS(25225614, 25225773, "-", "12", ""),
CDS(25209798, 25209911, "-", "12", "")
])
]),
Transcript(
25209168, 25250936, "-", "12", "KRAS-204",
{"id": "ENST00000557334"}, None, [
Exon(25250751, 25250936, "-", "12",
"ENST00000557334_e1"),
Exon(25245274, 25245395, "-", "12",
"ENST00000557334_e2"),
Exon(25209168, 25209911, "-", "12",
"ENST00000557334_e3")
], [
Protein(25209798, 25245384, "-", "12", None, None,
None, [
CDS(25245274, 25245384, "-", "12", ""),
CDS(25209798, 25209911, "-", "12", "")
])
]),
Transcript(
25209431, 25250803, "-", "12", "KRAS-201",
{"id": "ENST00000256078"}, None, [
Exon(25250751, 25250803, "-", "12",
"ENST00000256078_e1"),
Exon(25245274, 25245395, "-", "12",
"ENST00000256078_e2"),
Exon(25227234, 25227412, "-", "12",
"ENST00000256078_e3"),
Exon(25225614, 25225773, "-", "12",
"ENST00000256078_e4"),
Exon(25215437, 25215560, "-", "12",
"ENST00000256078_e5"),
Exon(25209431, 25209911, "-", "12",
"ENST00000256078_e6")
], [
Protein(25215444, 25245384, "-", "12", None, None,
None, [
CDS(25245274, 25245384, "-", "12", ""),
CDS(25227234, 25227412, "-", "12", ""),
CDS(25225614, 25225773, "-", "12", ""),
CDS(25215444, 25215560, "-", "12", "")
])
]),
Transcript(
25233819, 25250929, "-", "12", "KRAS-203",
{"id": "ENST00000556131"}, None, [
Exon(25250764, 25250929, "-", "12",
"ENST00000556131_e1"),
Exon(25245274, 25245395, "-", "12",
"ENST00000556131_e2"),
Exon(25233819, 25235226, "-", "12",
"ENST00000556131_e3")
], [
Protein(25235209, 25245384, "-", "12", None, None,
None, [
CDS(25245274, 25245384, "-", "12", ""),
CDS(25235209, 25235226, "-", "12", "")
])
])
])
]
with open(self.tmp_ensembl_in_gtf, "w") as FH_gtf:
FH_gtf.write("""#!genome-build GRCh38.p12
#!genome-version GRCh38
#!genome-date 2013-12
#!genome-build-accession NCBI:GCA_000001405.27
#!genebuild-last-updated 2018-07
6 havana gene 54770583 54771134 . + . gene_id \"ENSG00000220635\"; gene_version \"2\"; gene_name \"KRASP1\"; gene_source \"havana\"; gene_biotype \"processed_pseudogene\";
6 havana transcript 54770583 54771134 . + . gene_id \"ENSG00000220635\"; gene_version \"2\"; transcript_id \"ENST00000407852\"; transcript_version \"2\"; gene_name \"KRASP1\"; gene_source \"havana\"; gene_biotype \"processed_pseudogene\"; transcript_name \"KRASP1-201\"; transcript_source \"havana\"; transcript_biotype \"processed_pseudogene\"; tag \"basic\"; transcript_support_level \"NA\";
6 havana exon 54770583 54771134 . + . gene_id \"ENSG00000220635\"; gene_version \"2\"; transcript_id \"ENST00000407852\"; transcript_version \"2\"; exon_number \"1\"; gene_name \"KRASP1\"; gene_source \"havana\"; gene_biotype \"processed_pseudogene\"; transcript_name \"KRASP1-201\"; transcript_source \"havana\"; transcript_biotype \"processed_pseudogene\"; exon_id \"ENSE00001550689\"; exon_version \"2\"; tag \"basic\"; transcript_support_level \"NA\";
12 ensembl_havana gene 25204789 25250936 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\";
12 ensembl_havana transcript 25204789 25250931 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25250751 25250931 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00001189804\"; exon_version \"4\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25245274 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00000936617\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana CDS 25245274 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; protein_id \"ENSP00000308495\"; protein_version \"3\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana start_codon 25245382 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25227234 25227412 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00001719809\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana CDS 25227234 25227412 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; protein_id \"ENSP00000308495\"; protein_version \"3\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25225614 25225773 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"4\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00001644818\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana CDS 25225614 25225773 . - 1 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"4\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; protein_id \"ENSP00000308495\"; protein_version \"3\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25204789 25209911 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00002456976\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana CDS 25209798 25209911 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; protein_id \"ENSP00000308495\"; protein_version \"3\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana stop_codon 25209795 25209797 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana five_prime_utr 25250751 25250931 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana five_prime_utr 25245385 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana three_prime_utr 25204789 25209794 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\";
12 havana transcript 25209168 25250936 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\";
12 havana exon 25250751 25250936 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00002446502\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"5\";
12 havana exon 25245274 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00000936617\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"5\";
12 havana CDS 25245274 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; protein_id \"ENSP00000452512\"; protein_version \"1\"; tag \"basic\"; transcript_support_level \"5\";
12 havana start_codon 25245382 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\";
12 havana exon 25209168 25209911 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00002464674\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"5\";
12 havana CDS 25209798 25209911 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; protein_id \"ENSP00000452512\"; protein_version \"1\"; tag \"basic\"; transcript_support_level \"5\";
12 havana stop_codon 25209795 25209797 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\";
12 havana five_prime_utr 25250751 25250936 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\";
12 havana five_prime_utr 25245385 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\";
12 havana three_prime_utr 25209168 25209794 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\";
12 ensembl_havana transcript 25209431 25250803 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25250751 25250803 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00002513959\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25245274 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00000936617\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana CDS 25245274 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; protein_id \"ENSP00000256078\"; protein_version \"4\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana start_codon 25245382 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25227234 25227412 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00001719809\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana CDS 25227234 25227412 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; protein_id \"ENSP00000256078\"; protein_version \"4\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25225614 25225773 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"4\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00001644818\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana CDS 25225614 25225773 . - 1 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"4\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; protein_id \"ENSP00000256078\"; protein_version \"4\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25215437 25215560 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00001189807\"; exon_version \"5\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana CDS 25215444 25215560 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; protein_id \"ENSP00000256078\"; protein_version \"4\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana stop_codon 25215441 25215443 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana exon 25209431 25209911 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"6\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00002477035\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana five_prime_utr 25250751 25250803 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana five_prime_utr 25245385 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana three_prime_utr 25215437 25215440 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\";
12 ensembl_havana three_prime_utr 25209431 25209911 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\";
12 havana transcript 25233819 25250929 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"1\";
12 havana exon 25250764 25250929 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00002530521\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 havana exon 25245274 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00000936617\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 havana CDS 25245274 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; protein_id \"ENSP00000451856\"; protein_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 havana start_codon 25245382 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"1\";
12 havana exon 25233819 25235226 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00002478081\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 havana CDS 25235209 25235226 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; protein_id \"ENSP00000451856\"; protein_version \"1\"; tag \"basic\"; transcript_support_level \"1\";
12 havana stop_codon 25235206 25235208 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"1\";
12 havana five_prime_utr 25250764 25250929 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"1\";
12 havana five_prime_utr 25245385 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic; other\"; transcript_support_level \"1\";
12 havana three_prime_utr 25233819 25235205 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic;\"; transcript_support_level \"1\";"""
)
# NCBI GTF
self.ncbi_expected = [
Gene(54635272, 54640529, "+", "6", "KRASP1", {"id": "3844"}, None,
[
Transcript(
54635272, 54640529, "+", "6", "gene14201",
{"id": "gene14201"}, None,
[Exon(54635272, 54640529, "+", "6", "gene14201_e1")])
]),
Gene(25357723, 25403865, "-", "12", "KRAS", {"id": "3845"}, None, [
Transcript(
25357723, 25403865, "-", "12", "rna36549",
{"id": "rna36549"}, None, [
Exon(25357723, 25362845, "-", "12", "rna36549_e1"),
Exon(25378548, 25378707, "-", "12", "rna36549_e2"),
Exon(25380168, 25380346, "-", "12", "rna36549_e3"),
Exon(25398208, 25398329, "-", "12", "rna36549_e5"),
Exon(25403685, 25403865, "-", "12", "rna36549_e6")
], [
Protein(25362729, 25398318, "-", "12", None, None,
None, [
CDS(25362729, 25362845, "-", "12", ""),
CDS(25378548, 25378707, "-", "12", ""),
CDS(25380168, 25380346, "-", "12", ""),
CDS(25398208, 25398318, "-", "12", "")
])
]),
Transcript(25357723, 25403865, "-", "12", "rna36550", {
"id": "rna36550"
}, None, [
Exon(25357723, 25362845, "-", "12", "rna36550_e1"),
Exon(25368371, 25368494, "-", "12", "rna36550_e2"),
Exon(25378548, 25378707, "-", "12", "rna36550_e3"),
Exon(25380168, 25380346, "-", "12", "rna36550_e4"),
Exon(25398208, 25398329, "-", "12", "rna36550_e5"),
Exon(25403685, 25403865, "-", "12", "rna36550_e6")
], [
Protein(25368375, 25398318, "-", "12", None, None, None, [
CDS(25368375, 25368494, "-", "12", ""),
CDS(25378548, 25378707, "-", "12", ""),
CDS(25380168, 25380346, "-", "12", ""),
CDS(25398208, 25398318, "-", "12", ""),
])
])
]),
Gene(2527306, 2529079, "+", "X", "CD99P1", {"id": "401577"}, None,
[
Transcript(
2527306, 2529079, "+", "X", "rna58916",
{"id": "rna58916"}, None, [
Exon(2527306, 2527522, "+", "X", "rna58916_e1"),
Exon(2529037, 2529079, "+", "X", "rna58916_e2")
])
]),
Gene(2477306, 2479079, "+", "Y", "CD99P1", {"id": "401577"}, None,
[
Transcript(
2477306, 2479079, "+", "Y", "rna61353",
{"id": "rna61353"}, None, [
Exon(2477306, 2477522, "+", "Y", "rna61353_e1"),
Exon(2479037, 2479079, "+", "Y", "rna61353_e2")
])
])
]
with open(self.tmp_ncbi_in_gtf, "w") as FH_gtf:
FH_gtf.write(
"""6 Curated Genomic exon 54635272 54640529 . + . transcript_id \"gene14201\"; gene_id \"3844\"; gene_name \"KRASP1\";
12 BestRefSeq exon 25357723 25362845 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25378548 25378707 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25380168 25380346 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25398208 25398329 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25403685 25403865 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq CDS 25362729 25362845 . - 0 transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq CDS 25378548 25378707 . - 1 transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq CDS 25380168 25380346 . - 0 transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq CDS 25398208 25398318 . - 0 transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25357723 25362845 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25368371 25368494 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25378548 25378707 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25380168 25380346 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25398208 25398329 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq exon 25403685 25403865 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq CDS 25368375 25368494 . - 0 transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq CDS 25378548 25378707 . - 1 transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq CDS 25380168 25380346 . - 0 transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
12 BestRefSeq CDS 25398208 25398318 . - 0 transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\";
X BestRefSeq exon 2527306 2527522 . + . transcript_id \"rna58916\"; gene_id \"401577\"; gene_name \"CD99P1\";
X BestRefSeq exon 2529037 2529079 . + . transcript_id \"rna58916\"; gene_id \"401577\"; gene_name \"CD99P1\";
Y BestRefSeq exon 2477306 2477522 . + . transcript_id \"rna61353\"; gene_id \"401577\"; gene_name \"CD99P1\";
Y BestRefSeq exon 2479037 2479079 . + . transcript_id \"rna61353\"; gene_id \"401577\"; gene_name \"CD99P1\";"""
)