import os import json import re import pandas as pd import datasets from functools import cached_property logger = datasets.logging.get_logger(__name__) _CITATION = """\ @article{jolma2010multiplexed, title={Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities}, author={Jolma, Arttu and Kivioja, Teemu and Toivonen, Jarkko and Cheng, Lu and Wei, Gonghong and Enge, Martin and \ Taipale, Mikko and Vaquerizas, Juan M and Yan, Jian and Sillanp{\"a}{\"a}, Mikko J and others}, journal={Genome research}, volume={20}, number={6}, pages={861--873}, year={2010}, publisher={Cold Spring Harbor Lab} } """ _DESCRIPTION = """\ PRJEB3289 https://www.ebi.ac.uk/ena/browser/view/PRJEB3289 Data that has been generated by HT-SELEX experiments (see Jolma et al. 2010. PMID: 20378718 for description of method) \ that has been now used to generate transcription factor binding specificity models for most of the high confidence \ human transcription factors. Sequence data is composed of reads generated with Illumina Genome Analyzer IIX and \ HiSeq2000 instruments. Samples are composed of single read sequencing of synthetic DNA fragments with a fixed length \ randomized region or samples derived from such a initial library by selection with a sequence specific DNA binding \ protein. Originally multiple samples with different "barcode" tag sequences were run on the same Illumina sequencing \ lane but the released files have been already de-multiplexed, and the constant regions and "barcodes" of each sequence \ have been cut out of the sequencing reads to facilitate the use of data. Some of the files are composed of reads from \ multiple different sequencing lanes and due to this each of the names of the individual reads have been edited to show \ the flowcell and lane that was used to generate it. Barcodes and oligonucleotide designs are indicated in the names of \ individual entries. Depending of the selection ligand design, the sequences in each of these fastq-files are either \ 14, 20, 30 or 40 bases long and had different flanking regions in both sides of the sequence. Each run entry is named \ in either of the following ways: Example 1) "BCL6B_DBD_AC_TGCGGG20NGA_1", where name is composed of following fields \ ProteinName_CloneType_Batch_BarcodeDesign_SelectionCycle. This experiment used barcode ligand TGCGGG20NGA, where both \ of the variable flanking constant regions are indicated as they were on the original sequence-reads. This ligand has \ been selected for one round of HT-SELEX using recombinant protein that contained the DNA binding domain of \ human transcription factor BCL6B. It also tells that the experiment was performed on batch of experiments named as "AC".\ Example 2) 0_TGCGGG20NGA_0 where name is composed of (zero)_BarcodeDesign_(zero) These sequences have been generated \ from sequencing of the initial non-selected pool. Same initial pools have been used in multiple experiments that were \ on different batches, thus for example this background sequence pool is the shared background for all of the following \ samples. BCL6B_DBD_AC_TGCGGG20NGA_1, ZNF784_full_AE_TGCGGG20NGA_3, DLX6_DBD_Y_TGCGGG20NGA_4 and MSX2_DBD_W_TGCGGG20NGA_2 """ _URL = "ftp://ftp.sra.ebi.ac.uk/vol1/run/" "ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR173/ERR173154/CTCF_full_AJ_TAGCGA20NGCT_1.fastq.gz" # _FORWARD_PRIMER = "TAATACGACTCACTATAGGGAGCAGGAGAGAGGTCAGATG" # _REVERSE_PRIMER = "CCTATGCGTGCTAGTGTGA" # _DESIGN_LENGTH = 30 _DOWNLODE_MANAGER = datasets.DownloadManager() _RESOURCE_URL = "https://huggingface.co/datasets/thewall/DeepBindWeight/resolve/main" SELEX_INFO_FILE = _DOWNLODE_MANAGER.download(f"{_RESOURCE_URL}/ERP001824-deepbind.xlsx") pattern = re.compile("(\d+)") class JolmaConfig(datasets.BuilderConfig): def __init__(self, length_match=True, filter_N=True, **kwargs): super(JolmaConfig, self).__init__(**kwargs) self.length_match = length_match self.filter_N = filter_N class Jolma(datasets.GeneratorBasedBuilder): SELEX_INFO = pd.read_excel(SELEX_INFO_FILE, index_col=0) BUILDER_CONFIGS = [ JolmaConfig(name=index) for index in SELEX_INFO.index ] DEFAULT_CONFIG_NAME = "ERR173157" def _info(self): return datasets.DatasetInfo( description=_DESCRIPTION, features=datasets.Features( { "id": datasets.Value("int32"), "identifier": datasets.Value("string"), "seq": datasets.Value("string"), "quality": datasets.Value("string"), } ), homepage="https://www.ebi.ac.uk/ena/browser/view/PRJEB3289", citation=_CITATION, ) @cached_property def selex_info(self): return self.SELEX_INFO.loc[self.config.name] @cached_property def design_length(self): selex_info = self.selex_info return int(pattern.search(selex_info["Ligand"]).group(0)) def _split_generators(self, dl_manager): downloaded_files = None sra_id = self.config.name selex_info = self.selex_info file = selex_info['file'] if getattr(self.config, "data_dir") is not None: path = os.path.join(self.config.data_dir, sra_id, file) downloaded_files = dl_manager.extract(path) logger.info(f"Load from {downloaded_files}") if downloaded_files is None or not os.path.exists(downloaded_files): downloaded_url = "/".join([_URL, sra_id[:6], sra_id, file]) logger.info(f"Download from {downloaded_url}") downloaded_files = dl_manager.download_and_extract(downloaded_url) return [ datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files}), ] def _generate_examples(self, filepath): """This function returns the examples in the raw (text) form.""" logger.info("generating examples from = %s", filepath) key = 0 with open(filepath, encoding="utf-8") as f: ans = {"id": key} for i, line in enumerate(f): if line.startswith("@") and i%4==0: ans["identifier"] = line[1:].strip() elif i%4==1: ans["seq"] = line.strip() elif i%4==3: ans["quality"] = line.strip() if self.filter_fn(ans): yield key, ans key += 1 ans = {"id": key} def filter_fn(self, example): seq = example["seq"] if self.config.length_match and len(seq)!=self.design_length: return False if self.config.filter_N and "N" in seq: return False return True if __name__=="__main__": from datasets import load_dataset dataset = load_dataset("jolma.py", name="ERR173157", split="all") # dataset = load_dataset("jolma.py", name="ERR173157", split="all", data_dir="/root/autodl-fs/ERP001824-461")