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

default_sources:
  - "AffyProbes"
  - "BioGRID"
  - "EnsemblCompara"
  - "FlyBaseFasta"
  - "FlyBaseOrthologues"
  - "FlyOntologies"
  - "GOAnnotation"
  - "IntAct"
  - "IntactVocabulary"
  - "InterPro"
  - "InterProGO"
  - "MGIIdentifiers"
  - "NCBIGene"
  - "PDB"
  - "PubMed"
  - "Reactome"
  - "RedFly"
  - "RNAiScreens"
  - "UniProt"
  - "WormbaseRNAi"
  - "WormIdentifiers"

UniProt:
    organisms:
        - 83333
        - 511145
        - 1423
        - 224308
    excluded_organisms:
        - 10091
        - 10092
        - 35531
        - 39442
        - 46244
        - 57486
        - 63221
        - 116058
        - 180454
        - 377270
        - 377271
        - 377586
        - 377587
        - 943925
        - 943926
        - 316385
        - 1110693
        - 527799
        - 595496
        
<commit_msg>updated synbiomine download config #281<commit_after>log_dir: "/micklem/data/download_logs"
data_dir: "/micklem/data"

default_sources:
  - "BioGRID"
  - "GOAnnotation"
  - "IntAct"
  - "IntactVocabulary"
  - "InterPro"
  - "InterProGO"
  - "NCBIGene"
  - "PDB"
  - "PubMed"
  - "Reactome"
  - "UniProt"
  - "GenBank"

UniProt:
    organisms:
        - 83333
        - 511145
        - 1423
        - 224308
    excluded_organisms:
        - 10091
        - 10092
        - 35531
        - 39442
        - 46244
        - 57486
        - 63221
        - 116058
        - 180454
        - 377270
        - 377271
        - 377586
        - 377587
        - 943925
        - 943926
        - 316385
        - 1110693
        - 527799
        - 595496

GenBank:
    organisms:
        Bacteria:
        - Bacillus_subtilis_168_uid57675
        - Escherichia_coli_K_12_substr__MG1655_uid57779

{'fraction_non_alphanumeric': 0.10375275938189846, 'fraction_numerical': 0.1545253863134658, 'mean_word_length': 1.3545454545454545, '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': 3, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3100031', 'n_tokens_mistral': 930, 'n_tokens_neox': 695, 'n_words': 104}