<commit_before>log_dir: "/micklem/data/download_logs"
data_dir: "/micklem/data"

default_sources:
  - "BioGRID"
  - "FlyAnatomyOntology"
  - "FlyBaseFasta"
  - "FlyBaseOrthologues"
  - "FlyCVTerms"
  - "GOAnnotation"
  - "IntAct"
  - "IntActVocabulary"
  - "InterPro"
  - "InterProGO"
  - "MGIIdentifiers"
  - "NCBIGene"
  - "Panther"  
  - "PubMed"
  - "Reactome"
  - "RedFly"
  - "RGDIdentifiers"
  - "UniProt"
  - "WormIdentifiers"
  - "HomoloGene"
  - "OrthoDB"
  - "SGDIdentifiers"
  - "ZFINIdentifiers"
  - "MousePheno"
  - "HumanGeneIdentifiers"
  - "HPO"

UniProt:
    organisms:
        - 3702
        - 6239
        - 7165
        - 7217
        - 7220
        - 7222
        - 7227
        - 7230
        - 7234
        - 7238
        - 7240
        - 7244<commit_msg>add NCBI fasta download script. Refs #1259<commit_after>log_dir: "/tmp"
data_dir: "/micklem/data"

default_sources:
  - "BioGRID"
  - "FlyAnatomyOntology"
  - "FlyBaseFasta"
  - "FlyBaseOrthologues"
  - "FlyCVTerms"
  - "GOAnnotation"
  - "IntAct"
  - "IntActVocabulary"
  - "InterPro"
  - "InterProGO"
  - "MGIIdentifiers"
  - "NCBIGene"
  - "Panther"  
  - "PubMed"
  - "Reactome"
  - "RedFly"
  - "RGDIdentifiers"
  - "UniProt"
  - "WormIdentifiers"
  - "HomoloGene"
  - "OrthoDB"
  - "SGDIdentifiers"
  - "ZFINIdentifiers"
  - "MousePheno"
  - "HumanGeneIdentifiers"
  - "HPO"
  - "NCBIFasta"

UniProt:
    organisms:
        - 3702
        - 6239
        - 7165
        - 7217
        - 7220
        - 7222
        - 7227
        - 7230
        - 7234
        - 7238
        - 7240
        - 7244
{'fraction_non_alphanumeric': 0.13734177215189874, 'fraction_numerical': 0.06329113924050633, 'mean_word_length': 1.7591623036649215, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5099628', 'n_tokens_mistral': 778, 'n_tokens_neox': 677, 'n_words': 96}