def testBuildVariantID(self):
"""
Tests creation of variant id from
chrX:start-stop, ref_base, var_base or
chrX:start, ref_base, var_base
"""
data1=['chrX:12321', 'A', 'T']
data2=['chrX:1234-1256', 'G', 'C']
result01=build_variant_id(data1)
result02=build_variant_id(data2)
self.assertEquals(result01, 'X_12321_12321_A_T')
self.assertEquals(result02, 'X_1234_1256_G_C')
def add_links(Reader, sheet, fname):
"""
Process analysis file to add link columns
"""
#Need to get the pfx from the fname
(f_path, f_name) = os.path.split(fname)
f_short_name = f_name.replace('.SNP_Analysis.txt', '')
#rowx is the row#, row is the data
for rowx, row in enumerate(Reader):
variant_id, ref_reads, var_reads = build_variant_id(row)
row.insert(0, variant_id)
for colx, value in enumerate(row):
if colx == 0 and not value == 'gendb_link':
if len(value) < 198:
sheet.write_formula(
rowx, colx,
'HYPERLINK("https://gendb.labmed.uw.edu/genetics_db/search?variant_id={}","gendb_link")'
.format(value))
elif colx == 15 and not value == 'Faves_Y/N':
if len(value) < 198:
sheet.write_formula(
rowx, colx,
'HYPERLINK("https://control.labmed.uw.edu/var_clin/fav/?variant_id={}&pfx={}&ref_reads={}&var_reads={}","mark_fav")'
.format(variant_id, f_short_name, ref_reads,
var_reads))
else:
sheet.write(rowx, colx, float_if_possible(value))
def variant_id_link(Reader, sheet):
"""
Process analysis file to add link column
"""
for rowx, row in enumerate(Reader):
row.insert(0, build_variant_id(row))
for colx, value in enumerate(row):
if colx == 0 and not value == 'link':
if len(value) < 198:
sheet.write_formula(rowx, colx, 'HYPERLINK("https://apps.labmed.uw.edu/genetics_db/search?variant_id={}","link")'.format(value))
else:
sheet.write(rowx, colx, float_if_possible(value))
def testBuildVariantID(self):
"""
Tests creation of variant id and read count from
chrX:start-stop, ref_base, var_base or
chrX:start, ref_base, var_base
"""
#A bunch of empty 'columns' to represent the data in the SNP tab
data1 = [
'chrX:12321', 'A', 'T', '', '', '', '', '', '', '', '', '', '', '',
'', '10', '11'
]
data2 = [
'chrX:1234-1256', 'G', 'C', '', '', '', '', '', '', '', '', '', '',
'', '', '12', '13'
]
result01, ref_reads01, varreads01 = ann.build_variant_id(data1)
result02, ref_reads02, varreads02 = ann.build_variant_id(data2)
self.assertListEqual([result01, ref_reads01, varreads01],
['X_12321_12321_A_T', '10', '11'])
self.assertListEqual([result02, ref_reads02, varreads02],
['X_1234_1256_G_C', '12', '13'])
def variant_id_link(Reader, sheet):
"""
Process analysis file to add link column
"""
for rowx, row in enumerate(Reader):
row.insert(0, build_variant_id(row))
for colx, value in enumerate(row):
if colx == 0 and not value == 'link':
if len(value) < 198:
sheet.write_formula(
rowx, colx,
'HYPERLINK("https://apps.labmed.uw.edu/genetics_db/search?variant_id={}","link")'
.format(value))
else:
sheet.write(rowx, colx, float_if_possible(value))
def add_links(Reader, sheet, fname):
"""
Process analysis file to add link columns
"""
#Need to get the pfx from the fname
(f_path, f_name) = os.path.split(fname)
f_short_name = f_name.replace('.SNP_Analysis.txt','')
#rowx is the row#, row is the data
for rowx, row in enumerate(Reader):
variant_id, ref_reads, var_reads=build_variant_id(row)
row.insert(0, variant_id)
for colx, value in enumerate(row):
if colx == 0 and not value == 'gendb_link':
if len(value) < 198:
sheet.write_formula(rowx, colx, 'HYPERLINK("https://apps.labmed.uw.edu/genetics_db/search?variant_id={}","gendb_link")'.format(value))
elif colx == 15 and not value == 'Faves_Y/N':
if len(value) < 198:
sheet.write_formula(rowx, colx, 'HYPERLINK("https://kaos.labmed.uw.edu/var_clin/fav/?variant_id={}&pfx={}&ref_reads={}&var_reads={}","mark_fav")'.format(variant_id, f_short_name, ref_reads, var_reads))
else:
sheet.write(rowx, colx, float_if_possible(value))
