Update plant-multi-species-genomes.py
Browse files
plant-multi-species-genomes.py
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@@ -4,25 +4,36 @@ from 48 different species."""
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from typing import List
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import datasets
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import pandas as pd
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from Bio import SeqIO
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import os
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# Find for instance the citation on arxiv or on the dataset repo/website
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_CITATION = """
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# You can copy an official description
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_DESCRIPTION = """\
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Dataset made of diverse genomes available on NCBI and coming from 48 different species.
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Test and validation are made of 2 species each. The rest of the genomes are used for training.
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Default configuration "6kbp" yields chunks of 6.2kbp (100bp overlap on each side).The chunks of DNA are cleaned and processed so that
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they can only contain the letters A, T, C, G and N.
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"""
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_HOMEPAGE = "
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_LICENSE =
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_CHUNK_LENGTHS = [6000,]
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from typing import List
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import datasets
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from Bio import SeqIO
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import os
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# Find for instance the citation on arxiv or on the dataset repo/website
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_CITATION = """\
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@article{o2016reference,
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title={Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation},
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author={O'Leary, Nuala A and Wright, Mathew W and Brister, J Rodney and Ciufo, Stacy and Haddad, Diana and McVeigh, Rich and Rajput, Bhanu and Robbertse, Barbara and Smith-White, Brian and Ako-Adjei, Danso and others},
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journal={Nucleic acids research},
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volume={44},
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number={D1},
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pages={D733--D745},
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year={2016},
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publisher={Oxford University Press}
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}
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"""
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# You can copy an official description
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_DESCRIPTION = """\
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Dataset made of diverse genomes available on NCBI and coming from 48 different species.
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Test and validation are made of 2 species each. The rest of the genomes are used for training.
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Default configuration "6kbp" yields chunks of 6.2kbp (100bp overlap on each side). The chunks of DNA are cleaned and processed so that
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they can only contain the letters A, T, C, G and N.
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"""
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_HOMEPAGE = "https://www.ncbi.nlm.nih.gov/"
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_LICENSE = "https://www.ncbi.nlm.nih.gov/home/about/policies/"
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_CHUNK_LENGTHS = [6000,]
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