def test_3(self):
"""
"""
#test the dna and protein coding sequences are correct by comparing
#with manually generally sequences
fusion = agfusion.Fusion(
gene5prime="TMEM87B",
gene5primejunction=112843681,
gene3prime="MERTK",
gene3primejunction=112722771,
db=db_human,
pyensembl_data=data_human,
protein_databases=['pfam', 'tmhmm'],
noncanonical=False
)
fusion.save_transcript_cdna('TMEM87B-MERTK-case3')
fusion.save_transcript_cds('TMEM87B-MERTK-case3')
fusion.save_proteins('TMEM87B-MERTK-case3')
#fusion.save_images('DLG1-BRAF_mouse')
test_cds = open('./data/test-human-case-3.txt','r').read()
test_protein = Seq.Seq(test_cds,alphabet=Alphabet.generic_dna).translate()
test_protein = test_protein[0:test_protein.find('*')]
trans=fusion.transcripts['ENST00000283206-ENST00000295408']
assert test_cds==trans.cds.seq, "cds is wrongly predicted for human fusion (case 3)"
assert test_protein==trans.protein.seq, "protein is wrongly predicted for human fusion (case 3)"
def test_mouse_4(self):
"""
Test cDNA correctly produced for junctions being in UTRs
"""
fusion = agfusion.Fusion(
gene5prime="ENSMUSG00000022770",
gene5primejunction=31664851,
gene3prime="ENSMUSG00000022770",
gene3primejunction=31873343,
db=db,
pyensembl_data=data,
protein_databases=['pfam', 'tmhmm'],
noncanonical=True
)
cdna = 'GGGGGTGCGGCCGCCGAAGGGGGAGCTCCTCCCCCGTCCCCTCACCCCCTCAGCTGAGCT' + \
'CGGGGCGGGGCGGGGTACGTGGAGCGGGGCCGGGCGGGGAAGCTGCTCCGAGTCCGGCCG' + \
'GAGCGCACCCGGGGCGCCCGCGTACGCCGCTCGCGGGAACTTTGCGGCGGAGCCGCAGGT' + \
'GTGGAGGCCGCGGAGGGGGGTGCATGAGCGGCGCGGAGAGCGGCGGCTGTCCGGTCCGGC' + \
'CCCTGCTGGAGTCGCCGCCGGGAGGAGACGAACGAGGAACCAG' + \
'GTGTGTGCCGCCTTCCTGATTCTGGAGAAAA' + \
'AAAA'
assert str(fusion.transcripts['ENSMUST00000064477-ENSMUST00000064477'].cdna.seq)==cdna, "Test 4: cDNA wrong"
def annotate(gene5prime,
junction5prime,
gene3prime,
junction3prime,
agfusion_db,
pyensembl_data,
args,
outdir=None,
colors=None,
rename=None,
scale=None,
batch_out_dir=None):
"""
Annotate the gene fusion
"""
try:
fusion = agfusion.Fusion(gene5prime=gene5prime,
gene5primejunction=junction5prime,
gene3prime=gene3prime,
gene3primejunction=junction3prime,
db=agfusion_db,
pyensembl_data=pyensembl_data,
protein_databases=args.protein_databases,
noncanonical=args.noncanonical)
except IndexError:
#import IPython ; IPython.embed() ; raise
print('Problem for {} and {} fusion!'.format(gene5prime, gene3prime))
return
if batch_out_dir is not None:
outdir = join(
batch_out_dir,
fusion.gene5prime.gene.name + '-' + str(junction5prime) + '_' +
fusion.gene3prime.gene.name + '-' + str(junction3prime))
fusion.save_transcript_cdna(out_dir=outdir, middlestar=args.middlestar)
fusion.save_transcript_cds(out_dir=outdir, middlestar=args.middlestar)
fusion.save_proteins(out_dir=outdir, middlestar=args.middlestar)
fusion.save_images(out_dir=outdir,
file_type=args.type,
scale=scale,
colors=colors,
rename=rename,
fontsize=args.fontsize,
height=args.height,
width=args.width,
dpi=args.dpi,
no_domain_labels=args.no_domain_labels,
plot_WT=args.WT,
exclude=args.exclude_domain)
fusion.save_tables(out_dir=outdir)
def test_mouse_3(self):
fusion = agfusion.Fusion(
gene5prime="ENSMUSG00000022770",
gene5primejunction=31664850,
gene3prime="ENSMUSG00000002413",
gene3primejunction=39610381,
db=db,
pyensembl_data=data,
protein_databases=['pfam', 'tmhmm'],
noncanonical=True
)
assert fusion.transcripts['ENSMUST00000064477-ENSMUST00000002487'].effect_5prime=='5UTR',"Test 7: Not found in 5'UTR"
assert fusion.transcripts['ENSMUST00000064477-ENSMUST00000002487'].effect_3prime=='3UTR (start)', "Test 7: Not found in at 3'UTR beginning"
def test_mouse_7(self):
fusion = agfusion.Fusion(gene5prime="ENSMUSG00000022770",
gene5primejunction=31664820,
gene3prime="ENSMUSG00000002413",
gene3primejunction=39610405,
db=db,
pyensembl_data=data,
protein_databases=['pfam', 'tmhmm'],
noncanonical=True)
t = fusion.transcripts['ENSMUST00000023454-ENSMUST00000002487']
assert t.effect_5prime == "intron (before cds)", "Test 12: incorrect 5' effect: %s" % t.effect_5prime
assert t.effect_3prime == "intron (cds)", "Test 12: incorrect 3' effect: %s" % t.effect_3prime
def test_1(self):
"""
test CDS and cDNA correct for junction that is on exon boundaries and
produces an in-frame protein.
"""
#test the dna and protein coding sequences are correct by comparing
#with manually generally sequences
fusion = agfusion.Fusion(gene5prime="ENSMUSG00000022770",
gene5primejunction=31684294,
gene3prime="ENSMUSG00000002413",
gene3primejunction=39648486,
db=db,
pyensembl_data=data,
protein_databases=['pfam', 'tmhmm'],
noncanonical=True)
fusion.save_transcript_cdna('DLG1-BRAF_mouse')
fusion.save_transcript_cds('DLG1-BRAF_mouse')
fusion.save_proteins('DLG1-BRAF_mouse')
#fusion.save_images('DLG1-BRAF_mouse')
test_cdna = SeqIO.parse(open('./data/Dlg1-Braf_cdna_manual.fa', 'r'),
'fasta')
test_cds = SeqIO.parse(open('./data/Dlg1-Braf_cds_manual.fa', 'r'),
'fasta')
expected_transcript_combinations = [
'ENSMUST00000100001-ENSMUST00000002487',
'ENSMUST00000064477-ENSMUST00000002487',
'ENSMUST00000115205-ENSMUST00000002487',
'ENSMUST00000023454-ENSMUST00000002487',
'ENSMUST00000115201-ENSMUST00000002487',
'ENSMUST00000132176-ENSMUST00000002487'
]
assert len(
set(fusion.transcripts.keys()).intersection(
set(expected_transcript_combinations))
) == 6, "Test 1: unexpected number protein coding transcripts."
for seq in test_cdna:
trans = fusion.transcripts[str(seq.id)]
assert seq.seq == trans.cdna.seq, "cDNA is wrongly predicted: %s" % seq.id
for seq in test_cds:
trans = fusion.transcripts[str(seq.id)]
assert seq.seq == trans.cds.seq, "cds is wrongly predicted: %s" % seq.id
def test_1(self):
all_fusions = ['Adamts9-Ano2','Trp53-Sat2','1700112E06Rik-Runx1','Runx1-1700112E06Rik','Rell1-Lhfpl3','Phc1-Smarca2','Lrrc8d-Gbp11','C920009B18Rik-H60b']
for fusion in agfusion.parsers['fusioncatcher']('./data/FusionsFindingAlgorithms/FusionCatcher/final-list_candidate-fusion-genes.txt',db.logger):
fusion = agfusion.Fusion(
gene5prime=fusion['gene5prime'],
gene5primejunction=fusion['gene5prime_junction'],
gene3prime=fusion['gene3prime'],
gene3primejunction=fusion['gene3prime_junction'],
db=db,
pyensembl_data=data,
protein_databases=['pfam'],
noncanonical=False
)
assert fusion.name in all_fusions, '%s not in list!' % fusion.name
def test_mouse_1(self):
"""
Test that AGFusion determines if the effect on each individual transcript
"""
fusion = agfusion.Fusion(
gene5prime="ENSMUSG00000022770",
gene5primejunction=31664852,
gene3prime="ENSMUSG00000002413",
gene3primejunction=39651764,
db=db,
pyensembl_data=data,
protein_databases=['pfam', 'tmhmm'],
noncanonical=True
)
assert fusion.transcripts['ENSMUST00000064477-ENSMUST00000002487'].effect_5prime=='CDS (start)',"Test 5: not CDS start"
assert fusion.transcripts['ENSMUST00000064477-ENSMUST00000002487'].effect_3prime=='CDS',"Test 5: not CDS"
def test_3(self):
"""
Test CDS correct for junction within the exon (not on boundary) for one gene
one the forward and one gene on the reverse strand
"""
fusion = agfusion.Fusion(gene5prime="ENSMUSG00000022770",
gene5primejunction=31664869,
gene3prime="ENSMUSG00000002413",
gene3primejunction=39610402,
db=db,
pyensembl_data=data,
protein_databases=['pfam', 'tmhmm'],
noncanonical=True)
cds = 'ATGCCGGTCCGGAAGCAAGAATTTGCAGCCTTCAAGTAG'
assert str(fusion.transcripts['ENSMUST00000064477-ENSMUST00000002487'].
cds.seq) == cds, "Test 3: CDS wrong"
def annotate(gene5prime,junction5prime,gene3prime,junction3prime,
outdir,colors,rename,scale,db,pyensembl_data,args):
fusion = agfusion.Fusion(
gene5prime=gene5prime,
gene5primejunction=junction5prime,
gene3prime=gene3prime,
gene3primejunction=junction3prime,
db=db,
pyensembl_data=pyensembl_data,
protein_databases=args.protein_databases,
noncanonical=args.noncanonical
)
fusion.save_transcript_cdna(
out_dir=outdir,
middlestar=args.middlestar
)
fusion.save_transcript_cds(
out_dir=outdir,
middlestar=args.middlestar
)
fusion.save_proteins(
out_dir=outdir,
middlestar=args.middlestar
)
fusion.save_images(
out_dir=outdir,
scale=scale,
colors=colors,
rename=rename,
fontsize=args.fontsize,
height=args.height,
width=args.width,
dpi=args.dpi,
no_domain_labels=args.no_domain_labels,
plot_WT=args.WT,
exclude=args.exclude_domain
)
fusion.save_tables(out_dir=outdir)
def test_2(self):
"""
Test CDS correct for junction within the exon (not on boundary) for two
genes on reverse strand
"""
fusion = agfusion.Fusion(gene5prime="ENSMUSG00000002413",
gene5primejunction=39725110,
gene3prime="ENSMUSG00000002413",
gene3primejunction=39610402,
db=db,
pyensembl_data=data,
protein_databases=['pfam', 'tmhmm'],
noncanonical=True)
cds = 'ATGGCGGCGCTGAGTGGCGGCGGTGGCAGCAGCAGCGGTGGCGGCGGCGGCGGTGGCGGCGGCGG' + \
'TGGCGGTGGCGACGGCGGCGGCGGCGCCGAGCAGGGCCAGGCTCTGTTCAATGGCGACATGGAGC' + \
'CGGAGGCCGGCGCTGGCGCCGCGGCCTCTTCGGCTGCGGACCCGGCCATTCCTGAAGAATTTGCAGCCTTCAAGTAG'
assert str(fusion.transcripts['ENSMUST00000002487-ENSMUST00000002487'].
cds.seq) == cds, "Test 2: CDS wrong"
def test_mouse_5(self):
fusion = agfusion.Fusion(gene5prime="ENSMUSG00000022770",
gene5primejunction=31664850,
gene3prime="ENSMUSG00000002413",
gene3primejunction=39603240,
db=db,
pyensembl_data=data,
protein_databases=['pfam', 'tmhmm'],
noncanonical=True)
cdna = 'GGGGGTGCGGCCGCCGAAGGGGGAGCTCCTCCCCCGTCCCCTCACCCCCTCAGCTGAGCT' + \
'CGGGGCGGGGCGGGGTACGTGGAGCGGGGCCGGGCGGGGAAGCTGCTCCGAGTCCGGCCG' + \
'GAGCGCACCCGGGGCGCCCGCGTACGCCGCTCGCGGGAACTTTGCGGCGGAGCCGCAGGT' + \
'GTGGAGGCCGCGGAGGGGGGTGCATGAGCGGCGCGGAGAGCGGCGGCTGTCCGGTCCGGC' + \
'CCCTGCTGGAGTCGCCGCCGGGAGGAGACGAACGAGGAACCAG' + \
'GTGTGTGCCGCCTTCCTGATTCTGGAGAAA' + \
'GAAA'
assert str(fusion.transcripts['ENSMUST00000064477-ENSMUST00000002487'].
cdna.seq) == cdna, "Test 10: incorrect cDNA"
def index():
params = {}
params['gene5prime'] = ""
params['gene3prime'] = ""
params['loc5prime'] = ""
params['loc3prime'] = ""
params['grcm38_color'] = "white"
params['grch37_color'] = "white"
params['grch38_color'] = "white"
params['fontsize'] = "12"
params['dpi'] = "100"
params['imagewidth'] = "8"
params['imageheight'] = "2"
params['scale'] = "0"
params['genome'] = "GRCm38"
params['plotdisplay'] = 'none'
params['inputerror'] = 'hidden'
params['optionalparameterdisplay'] = 'none'
if 'id' not in session:
session['id'] = str(uuid.uuid4())
session['userdata'] = os.path.join(os.path.abspath(os.curdir),
'userdata', session['id'])
if not os.path.exists(session['userdata']):
os.mkdir(session['userdata'])
if 'submitfusion' in request.form:
params['gene5prime'] = str(request.form['gene5prime'])
params['gene3prime'] = str(request.form['gene3prime'])
params['loc5prime'] = str(request.form['loc5prime'])
params['loc3prime'] = str(request.form['loc3prime'])
params['fontsize'] = str(request.form['fontsize'])
params['dpi'] = str(request.form['dpi'])
params['imagewidth'] = str(request.form['imagewidth'])
params['imageheight'] = str(request.form['imageheight'])
params['scale'] = str(request.form['scale'])
params['genome'] = str(request.form['genome'])
params['inputerror'] = 'hidden'
params, pyensembl_data = set_genome(params)
params, error = check_fusion_input(params=params)
if error is not None:
return error
params, error = check_params(params=params)
if error is not None:
return error
#try to construct the fusion
try:
fusion = agfusion.Fusion(
gene5prime=params['gene5prime'],
gene5primejunction=int(params['loc5prime']),
gene3prime=params['gene3prime'],
gene3primejunction=int(params['loc3prime']),
db=db,
pyensembl_data=pyensembl_data)
except agfusion.exceptions.GeneIDException5prime as e:
params['inputerrormsg'] = e
params['inputerror'] = 'visible'
return render_template('index.html', params=params)
except agfusion.exceptions.GeneIDException3prime as e:
params['inputerrormsg'] = e
params['inputerror'] = 'visible'
return render_template('index.html', params=params)
except agfusion.exceptions.JunctionException5prime as e:
params['inputerrormsg'] = e
params['inputerror'] = 'visible'
return render_template('index.html', params=params)
except agfusion.exceptions.JunctionException3prime as e:
params['inputerrormsg'] = e
params['inputerror'] = 'visible'
return render_template('index.html', params=params)
except agfusion.exceptions.TooManyGenesException as e:
params['inputerrormsg'] = e
params['inputerror'] = 'visible'
return render_template('index.html', params=params)
#save the fusion output and visualize
middlestar = False
fusion.save_transcript_cdna(out_dir=session['userdata'],
middlestar=middlestar)
fusion.save_transcript_cds(out_dir=session['userdata'],
middlestar=middlestar)
fusion.save_proteins(out_dir=session['userdata'],
middlestar=middlestar)
pickle.dump(fusion, open(session['userdata'] + '/fusion.pk', 'wb'))
session['name'] = fusion.name
dict_of_plots, plot_key = fusion.output_to_html(
fontsize=params['fontsize'],
dpi=params['dpi'],
width=params['imagewidth'],
height=params['imageheight'],
scale=params['scale'],
mpld3=mpld3)
effects = {}
for name, transcript in fusion.transcripts.items():
effects[name] = {
'effect': transcript.effect,
'5prime_effect': transcript.effect_5prime,
'3prime_effect': transcript.effect_3prime
}
session['plot_key'] = plot_key
params['plotdisplay'] = 'visible'
params['name'] = fusion.name
params['gene5prime'] = params['gene5prime'].upper()
params['gene3prime'] = params['gene3prime'].upper()
return render_template('index.html',
dict_of_plots=dict_of_plots,
effects=effects,
params=params)
elif 'downloadseq' in request.form:
#download sequence data
if request.form['downloadseq'] == 'cdna':
return send_file(session['userdata'] + '/' + session['name'] +
'_cdna.fa',
as_attachment=True)
elif request.form['downloadseq'] == 'cds':
return send_file(session['userdata'] + '/' + session['name'] +
'_cds.fa',
as_attachment=True)
else:
return send_file(session['userdata'] + '/' + session['name'] +
'_protein.fa',
as_attachment=True)
elif 'downloadimage' in request.form:
params['fontsize'] = str(request.form['fontsize'])
params['dpi'] = str(request.form['dpi'])
params['imagewidth'] = str(request.form['imagewidth'])
params['imageheight'] = str(request.form['imageheight'])
params['scale'] = str(request.form['scale'])
params['inputerror'] = 'hidden'
params['plotdisplay'] = 'visible'
params, error = check_params(params=params)
if error is not None:
return error
#download image data
fusion = pickle.load(open(session['userdata'] + '/fusion.pk', 'rb'))
fusion_name = str(request.form['image_key'])
image_file = fusion.save_image(transcript=fusion_name,
out_dir=session['userdata'],
file_type=str(
request.form['downloadimage']),
fontsize=params['fontsize'],
dpi=params['dpi'],
width=params['imagewidth'],
height=params['imageheight'],
scale=params['scale'])
return send_file(image_file, as_attachment=True)
else:
# default index load
return render_template('index.html', params=params)
