def test_all(self):
expected = '>ACACA--STAC2'
fasta_path = str(
(pathlib.Path(__file__).parent / 'data/finspector.fa').resolve())
data = fasta.get_data(fasta_path)
self.assertTrue(data.startswith(expected))
def test_region(self):
region = 'ACACA--STAC2:61-70'
expected = 'ACAAATATTA'
data = fasta.get_data('data/finspector.fa', region)
self.assertTrue(data)
self.assertEqual(expected, data)
def test_remote(self):
data = fasta.get_data(
"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
{
"chr": "chr1",
"start": 100,
"end": 200
})
self.assertTrue(data)
def create_report(args):
variants_file = args.sites
if variants_file.endswith(".vcf") or variants_file.endswith(".vcf.gz"):
table = VariantTable(variants_file, args.info_columns,
args.info_columns_prefixes, args.sample_columns)
elif variants_file.endswith(".bed") or variants_file.endswith(".bed.gz"):
if args.type is not None and args.type == "junction":
table = JunctionBedTable(variants_file, args.info_columns)
else:
table = BedTable(variants_file)
table_json = table.to_JSON()
session_dict = {}
# Create file readers for tracks. This is done outside the loop so initialization happens onc
trackreaders = []
if args.tracks is not None:
for track in args.tracks:
reader = utils.getreader(track)
trackreaders.append({"track": track, "reader": reader})
trackconfigs = []
if args.track_config is not None:
for trackobj in args.track_config:
with open(trackobj) as f:
data = json.load(f)
for config in data:
reader = utils.getreader(config["url"])
trackconfigs.append({"config": config, "reader": reader})
# loop through variants creating an igv.js session for each one
flanking = 0
if args.flanking is not None:
flanking = float(args.flanking)
for tuple in table.features:
feature = tuple[0]
unique_id = tuple[1]
if hasattr(feature, "session_id"):
session_id = feature.session_id
else:
session_id = str(unique_id)
if session_id not in session_dict:
# Define a genomic region around the variant
if hasattr(feature, "viewport"):
region = parse_region(feature.viewport)
chr = region["chr"]
start = region["start"]
end = region["end"]
else:
chr = feature.chr
start = int(math.floor(feature.start - flanking / 2))
end = int(math.ceil(feature.end + flanking / 2))
region = {"chr": chr, "start": start, "end": end}
# Fasta
data = fasta.get_data(args.fasta, region)
fa = '>' + chr + ':' + str(start) + '-' + str(end) + '\n' + data
fasta_uri = datauri.get_data_uri(fa)
fastaJson = {
"fastaURL": fasta_uri,
}
# Ideogram
if (args.ideogram):
ideo_string = ideogram.get_data(args.ideogram, region)
ideo_uri = datauri.get_data_uri(ideo_string)
fastaJson["cytobandURL"] = ideo_uri
# Initial locus, +/- 20 bases
if (hasattr(feature, "viewport")):
initial_locus = feature.viewport
else:
position = int(math.floor(
(feature.start + feature.end) /
2)) + 1 # center of region in 1-based coordinates
initial_locus = chr + ":" + str(position -
20) + "-" + str(position + 20)
session_json = {
"locus": initial_locus,
"reference": fastaJson,
"tracks": []
}
for tr in trackreaders:
track = tr["track"]
reader = tr["reader"]
trackobj = tracks.get_track_json_dict(track)
data = reader.slice(region)
trackobj["url"] = datauri.get_data_uri(data)
if (trackobj["type"] == "alignment"):
trackobj["height"] = 500
# Sort TODO -- do this only for SNV
# if (trackObj["type"]) == "alignment":
# trackObj["sort"] = {
# "option": "NUCLEOTIDE",
# "locus": chr + ":" + str(variant.pos - 1)
# }
session_json["tracks"].append(trackobj)
for tc in trackconfigs:
trackobj = tc["config"]
if "name" not in trackobj:
trackobj["name"] = trackobj["url"]
reader = tc["reader"]
data = reader.slice(region)
trackobj["url"] = datauri.get_data_uri(data)
session_json["tracks"].append(trackobj)
# Build the session data URI
session_string = json.dumps(session_json)
session_uri = datauri.get_data_uri(session_string)
session_dict[session_id] = session_uri
session_dict = json.dumps(session_dict)
template_file = args.template
if None == template_file:
if 'junction' == args.type:
template_file = os.path.dirname(
sys.modules['igv_reports'].__file__
) + '/templates/junction_template.html'
else:
template_file = os.path.dirname(
sys.modules['igv_reports'].__file__
) + '/templates/variant_template.html'
output_file = args.output
standalone = args.standalone
with open(template_file, "r") as f:
data = f.readlines()
with open(output_file, "w") as o:
for i, line in enumerate(data):
if args.title is not None and line.startswith("<!--title-->"):
o.write("<h1>" + args.title + "</h1>")
if standalone:
if line.strip().startswith("<script") and ".js\"" in line:
inline_script(line, o, "js")
continue
elif line.strip().startswith(
"<link") and line.strip().endswith("css\">"):
inline_script(line, o, "css")
continue
j = line.find('"@TABLE_JSON@"')
if j >= 0:
line = line.replace('"@TABLE_JSON@"', table_json)
j = line.find('"@SESSION_DICTIONARY@"')
if j >= 0:
line = line.replace('"@SESSION_DICTIONARY@"', session_dict)
o.write(line)
def create_report(args):
variants_file = args.sites
if variants_file.endswith(".vcf") or variants_file.endswith(".vcf.gz"):
table = VariantTable(variants_file, args.species, args.info_columns,
args.info_columns_prefixes, args.sample_columns)
elif variants_file.endswith(".bed") or variants_file.endswith(".bed.gz"):
table = BedTable(variants_file)
table_json = table.to_JSON()
session_dict = {}
# Create file readers for tracks. This is done outside the loop so initialization happens onc
trackreaders = []
if args.tracks is not None:
for track in args.tracks:
reader = utils.getreader(track)
trackreaders.append({"track": track, "reader": reader})
# loop through variants creating an igv.js session for each one
for tuple in table.features:
feature = tuple[0]
unique_id = tuple[1]
# Define a genomic region around the variant
chr = feature.chr
position = int(math.floor(
(feature.start + feature.end) /
2)) + 1 # center of region in 1-based coordinates
start = int(math.floor(feature.start - int(args.flanking) / 2))
end = int(math.ceil(feature.end + int(args.flanking) / 2))
region = {"chr": chr, "start": start, "end": end}
# Fasta
data = fasta.get_data(args.fasta, region)
fa = '>' + chr + ':' + str(start) + '-' + str(end) + '\n' + data
fasta_uri = datauri.get_data_uri(fa)
fastaJson = {
"fastaURL": fasta_uri,
}
# Ideogram
if (args.ideogram):
ideo_string = ideogram.get_data(args.ideogram, region)
ideo_uri = datauri.get_data_uri(ideo_string)
fastaJson["cytobandURL"] = ideo_uri
# Initial locus, +/- 20 bases
initial_locus = chr + ":" + str(position - 20) + "-" + str(position +
20)
session_json = {
"locus": initial_locus,
"reference": fastaJson,
"tracks": []
}
for tr in trackreaders:
track = tr["track"]
reader = tr["reader"]
trackObj = tracks.get_track_json_dict(track)
data = reader.slice(region)
trackObj["url"] = datauri.get_data_uri(data)
if (trackObj["type"] == "alignment"):
trackObj["height"] = 500
# Sort TODO -- do this only for SNV
# if (trackObj["type"]) == "alignment":
# trackObj["sort"] = {
# "option": "NUCLEOTIDE",
# "locus": chr + ":" + str(variant.pos - 1)
# }
session_json["tracks"].append(trackObj)
# Build the session data URI
session_string = json.dumps(session_json)
session_uri = datauri.get_data_uri(session_string)
session_dict[str(unique_id)] = session_uri
session_dict = json.dumps(session_dict)
template_file = args.template
if None == template_file:
template_file = os.path.dirname(sys.modules['igv_reports'].__file__
) + '/templates/variant_template.html'
output_file = args.output
standalone = args.standalone
with open(template_file, "r") as f:
data = f.readlines()
with open(output_file, "w") as o:
for i, line in enumerate(data):
if standalone and "<script" in line and line.find(".js") > 0:
inline_script(line, o)
else:
j = line.find('"@TABLE_JSON@"')
if j >= 0:
line = line.replace('"@TABLE_JSON@"', table_json)
j = line.find('"@SESSION_DICTIONARY@"')
if j >= 0:
line = line.replace('"@SESSION_DICTIONARY@"',
session_dict)
o.write(line)