def main():
args = init_opt()
(psmsummary, pepsummary)=xls_tidy(args.input,args.qvalue)
etl.totsv(psmsummary, args.outprefix+"-psmSummary.tsv")
etl.totsv(pepsummary, args.outprefix+"-pepSummary.tsv")
out=open(args.outprefix+"-sequence.fa", 'w')
proid={x.split(";")[0]:True for x in pepsummary['Protein']} #get the first protein id
for header, seq in fasta_iter(args.db):
if(header in proid):
out.write(">%s\n%s\n" %(header,seq))
out.close()
def test_ZipSource():
# setup
table = [('foo', 'bar'), ('a', '1'), ('b', '2')]
totsv(table, 'tmp/issue_241.tsv')
z = zipfile.ZipFile('tmp/issue_241.zip', mode='w')
z.write('tmp/issue_241.tsv', 'data.tsv')
z.close()
# test
actual = fromtsv(ZipSource('tmp/issue_241.zip', 'data.tsv'))
ieq(table, actual)
def test_ZipSource():
# setup
table = [('foo', 'bar'), ('a', '1'), ('b', '2')]
totsv(table, 'tmp/issue_241.tsv')
z = zipfile.ZipFile('tmp/issue_241.zip', mode='w')
z.write('tmp/issue_241.tsv', 'data.tsv')
z.close()
# test
actual = fromtsv(ZipSource('tmp/issue_241.zip', 'data.tsv'))
ieq(table, actual)
def test_issue_231():
table = [['foo', 'bar'], ['a', '1'], ['b', '2']]
t = cut(table, 'foo')
totsv(t, 'tmp/issue_231.tsv')
u = fromtsv('tmp/issue_231.tsv')
ieq(t, u)
tocsv(t, 'tmp/issue_231.csv')
u = fromcsv('tmp/issue_231.csv')
ieq(t, u)
topickle(t, 'tmp/issue_231.pickle')
u = frompickle('tmp/issue_231.pickle')
ieq(t, u)
def test_issue_231():
table = [['foo', 'bar'], ['a', '1'], ['b', '2']]
t = cut(table, 'foo')
totsv(t, 'tmp/issue_231.tsv')
u = fromtsv('tmp/issue_231.tsv')
ieq(t, u)
tocsv(t, 'tmp/issue_231.csv')
u = fromcsv('tmp/issue_231.csv')
ieq(t, u)
topickle(t, 'tmp/issue_231.pickle')
u = frompickle('tmp/issue_231.pickle')
ieq(t, u)
def test_zipsource():
# setup
tbl = [('foo', 'bar'), ('a', '1'), ('b', '2')]
fn_tsv = NamedTemporaryFile().name
etl.totsv(tbl, fn_tsv)
fn_zip = NamedTemporaryFile().name
z = zipfile.ZipFile(fn_zip, mode='w')
z.write(fn_tsv, 'data.tsv')
z.close()
# test
actual = etl.fromtsv(ZipSource(fn_zip, 'data.tsv'))
ieq(tbl, actual)
def test_zipsource():
# setup
tbl = [('foo', 'bar'), ('a', '1'), ('b', '2')]
fn_tsv = NamedTemporaryFile().name
etl.totsv(tbl, fn_tsv)
fn_zip = NamedTemporaryFile().name
z = zipfile.ZipFile(fn_zip, mode='w')
z.write(fn_tsv, 'data.tsv')
z.close()
# test
actual = etl.fromtsv(ZipSource(fn_zip, 'data.tsv'))
ieq(tbl, actual)
def test_totsv_appendtsv():
# exercise function
table = (("foo", "bar"), ("a", 1), ("b", 2), ("c", 2))
f = NamedTemporaryFile(delete=False)
totsv(table, f.name)
# check what it did
with open(f.name, "rb") as o:
actual = csv.reader(o, delimiter="\t")
expect = [["foo", "bar"], ["a", "1"], ["b", "2"], ["c", "2"]]
ieq(expect, actual)
# check appending
table2 = (("foo", "bar"), ("d", 7), ("e", 9), ("f", 1))
appendtsv(table2, f.name)
# check what it did
with open(f.name, "rb") as o:
actual = csv.reader(o, delimiter="\t")
expect = [["foo", "bar"], ["a", "1"], ["b", "2"], ["c", "2"], ["d", "7"], ["e", "9"], ["f", "1"]]
ieq(expect, actual)
def test_totsv_appendtsv():
# exercise function
table = (('foo', 'bar'), ('a', 1), ('b', 2), ('c', 2))
f = NamedTemporaryFile(delete=False)
totsv(table, f.name)
# check what it did
with open(f.name, 'rb') as o:
actual = csv.reader(o, delimiter='\t')
expect = [['foo', 'bar'], ['a', '1'], ['b', '2'], ['c', '2']]
ieq(expect, actual)
# check appending
table2 = (('foo', 'bar'), ('d', 7), ('e', 9), ('f', 1))
appendtsv(table2, f.name)
# check what it did
with open(f.name, 'rb') as o:
actual = csv.reader(o, delimiter='\t')
expect = [['foo', 'bar'], ['a', '1'], ['b', '2'], ['c', '2'],
['d', '7'], ['e', '9'], ['f', '1']]
ieq(expect, actual)
def test_totsv_appendtsv():
# exercise function
table = (('foo', 'bar'),
('a', 1),
('b', 2),
('c', 2))
f = NamedTemporaryFile(delete=False)
totsv(table, f.name)
# check what it did
with open(f.name, 'rb') as o:
actual = csv.reader(o, delimiter='\t')
expect = [['foo', 'bar'],
['a', '1'],
['b', '2'],
['c', '2']]
ieq(expect, actual)
# check appending
table2 = (('foo', 'bar'),
('d', 7),
('e', 9),
('f', 1))
appendtsv(table2, f.name)
# check what it did
with open(f.name, 'rb') as o:
actual = csv.reader(o, delimiter='\t')
expect = [['foo', 'bar'],
['a', '1'],
['b', '2'],
['c', '2'],
['d', '7'],
['e', '9'],
['f', '1']]
ieq(expect, actual)
import petl as etl
readFile = etl.fromtsv("donedeal_data_sample.tsv")
tmpTable = etl.addfield(readFile, 'InKms', lambda rec: rec['mileage'])
tmpTable2File = etl.convert(tmpTable,
'InKms',
lambda v: int(float(v) * 1.6),
where=lambda r: r.mileageType == 'miles')
etl.totsv(tmpTable2File, 'donedeal_inKms.tsv')
import petl as etl
table1 = etl.fromtsv("D:\JOB\BI_Developer_Challenge\donedeal_data_sample.tsv")
table2 = etl.convert(table1, 'mileage', float)
table3 = etl.convert(table2,
'mileage',
lambda v: v * 1.60934,
where=lambda r: r.mileageType == 'miles')
table4 = etl.convert(table3,
'mileageType',
lambda v: 'km',
where=lambda r: r.mileageType in ('miles', 'kilometres'))
table4 = etl.convert(table3,
'mileageType',
lambda v: 'NA',
where=lambda r: r.mileageType not in ('km'))
etl.totsv(table4, "D:\JOB\BI_Developer_Challenge\donedeal_data_etl.tsv")
