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bedtable.py
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bedtable.py
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import json
import html
from .feature import parse
class BedTable:
# Always remember the *self* argument
def __init__(self, bed_file):
self.features = []
featureList = parse(bed_file)
unique_id = 0
self.has_name = False
for feature in featureList:
if len(feature.name) > 0:
self.has_name = True
self.features.append((feature, unique_id))
unique_id += 1
def to_JSON(self):
headers = ["unique_id", "Chrom", "Start", "End"]
if self.has_name:
headers.append("Name")
rows = []
for tuple in self.features:
feature = tuple[0]
unique_id = tuple[1]
rows.append([unique_id, feature.chr, feature.start+1, feature.end, html.escape(feature.name)])
return json.dumps({
"headers": headers,
"rows": rows
})
class BedpeTable:
# Always remember the *self* argument
def __init__(self, bedpe_file):
self.features = []
featureList = parse(bedpe_file)
unique_id = 0
self.has_name = False
for feature in featureList:
if len(feature.name) > 0:
self.has_name = True
self.features.append((feature, unique_id))
unique_id += 1
def to_JSON(self):
headers = ["unique_id", "Chrom_A", "Start_A", "End_A", "Chrom_B", "Start_B", "End_B"]
if self.has_name:
headers.append("Name")
rows = []
for tuple in self.features:
feature = tuple[0]
unique_id = tuple[1]
rows.append([unique_id, feature.chr, feature.start+1, feature.end, feature.chr2, feature.start2+1, feature.end2, html.escape(feature.name)])
return json.dumps({
"headers": headers,
"rows": rows
})
class JunctionBedTable:
# Always remember the *self* argument
def __init__(self, bed_file, info_columns = None):
self.features = []
self.table_columns = info_columns or None
featureList = parse(bed_file)
unique_id = 1
session_id = 1
viewport_to_session_id = {}
for f in featureList:
#expand name field
name_tokens = f.name.split(";")
for token in name_tokens:
kv = token.split("=")
key = kv[0]
value = kv[1]
setattr(f, key, value)
# Junction report variants are defined in rows with "viewport" attributes. Its possible multiple variants
# share the same viewport, if this is the case they can share a session. This is a space optimization.
if hasattr(f, 'viewport'):
self.features.append((f, unique_id))
unique_id += 1
viewport = f.viewport
if viewport in viewport_to_session_id:
sid = viewport_to_session_id[viewport]
else:
sid = str(session_id)
viewport_to_session_id[viewport] = sid
session_id += 1
f.session_id = sid
def to_JSON(self):
json_array = [];
id_to_session = {}
for tuple in self.features:
feature = tuple[0]
name_tokens = feature.name.split(";")
unique_id = tuple[1]
id_to_session[unique_id] = feature.session_id
obj = {
"unique_id": unique_id,
"session_id": feature.session_id,
"viewport": feature.viewport,
"feature_locus": feature.chr + ":" + str(feature.start) + "-" + str(feature.end),
"Chrom": feature.chr,
"Start": feature.start + 1,
"End": feature.end
}
if self.table_columns == None:
for token in name_tokens:
kv = token.split("=")
key = kv[0]
if key != 'viewport':
value = kv[1]
obj[key] = value
else:
dict = {}
for token in name_tokens:
kv = token.split("=")
dict[kv[0]] = kv[1]
for key in self.table_columns:
if key in dict:
obj[key] = dict[key]
else:
obj[key] = ''
json_array.append(obj)
normalized = normalize_json(self.table_columns, json_array)
normalized["id_to_session"] = id_to_session
return json.dumps(normalized)
def normalize_json(info_fields, json_array):
headers = ['unique_id', 'CHROM', 'POSITION', 'REF', 'ALT', 'ID']
if info_fields is not None:
for h in info_fields:
if h == 'ANN':
headers = headers + [ 'GENE', 'EFFECTS', 'IMPACT', 'TRANSCRIPT', 'GENE_ID', 'PROTEIN ALTERATION', 'DNA ALTERATION']
else:
headers.append(h)
rows = []
for json in json_array:
r = []
for h in headers:
if h in json:
r.append(json[h])
else:
r.append("")
rows.append(r)
return {
"headers": headers,
"rows": rows
}