ioligo

OLIGO5

Python object composed of oligo. The oligo database file based on the h5 file structure can contain one or more oligo files(tests/test_data/sample.oligo5).


from ioligo import OLIGO5

oligo5_test = OLIGO5("test")
oligo5_file = "tests/test_data/oligo/test.oligo5"
oligo5_test.read(oligo5_file)

oligo5_test.name
# 'test'
oligo5_test.oligos
# {'G-sample': [<oligo.oligo.OLIGO object at 0x7fcb26336a30>]}
type(oligo5_test.oligos["G-sample"])
# <class 'list'>
oligo5_test.oligos["G-sample"][0].name
# 'sample'
olgio5_test.help()
# "more info: https://github.com/iOLIGO/oligo/blob/main/docs/oligo5.md"
oligo5_test.info()
# 'test_info.tsv'

info formate

groups	oligos	number
group1	oligo1,oligo2,…oligon	number1,number2,…,numbern
group2	oligo1,oligo2,…oligon	number1,number2,…,numbern
…	…	…
groupn	oligo1,oligo2,…oligon	number1,number2,…,numbern

More usage

Read multiple oligo files at the same time to form an oligo5 file.

oligo1 = "./test.oligo"
oligo2 = "./test/test2.oligo"
oligo3 = "./test/test3.oligo"
from ioligo import OLIGO5
oligo5_test = OLIGO5("test")
oligo5_test.read_foligo(oligo1, oligo2, oligo3)

Read all oligo files in the directory at the same time to form an oligo5 file.

oligos_dir = "./test"
from ioligo import OLIGO5
oligo5_test = OLIGO5("test")
oligo5_test.read_doligo(oligos_dir)

Perform statistics on data sets in oligo5

1	oligo5_test.info("test_data/oligo/doligo5")

Output as oligo5 file

1
2
3


oligo5.to_oligo5("test_data/oligo/doligo")

Output as oligo dir

1	oligo5.to_oligo("test_data/oligo/O5toO")