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ioligo

Currently, there are very few file formats and database formats for saving oligonucleotides (probes). Most files are saved in bed or tsv format. However, this is extremely unfriendly for recording the source of oligonucleotides and subsequent processing in standard procedures.

Features

ioligo can change this situation.

  • oligo: simultaneously record the sequence information and characteristic information of the oligonucleotide in oligo format, such as the source species, which tools are used, and parameter design.
  • oligo5: one or more oligonucleotide files are designed to be compressed and saved in the oligo5 format based on the h5 file format.

Installation

To install ioligo with github:

pip

pip install ioligo

usage

CLI

ioligo --help

# oligo to oligo5
ioligo -ft OstoO5 -o test_data/oligo/test.oligo -n5 test_cli -ot test_data/oligo

# oligo dir to oligo5
ioligo -ft OstoO5 -od test_data/oligo -n5 test_cli_dir -ot test_data/oligo

# oligo5 ot oligo
ioligo -ft O5toOs -o5 test_data/oligo/test_cli_dir.oligo5 -ot test_data/oligo/O5toOs_cli

API

from ioligo import OLIGO,OLIGO5

More usage help

jupyter sample

more sample: https://github.com/iOLIGO/oligo/blob/main/tests/oligo.ipynb