<commit_before>dm6:
  gtf:
    url: 'ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gtf/dmel-all-r6.11.gtf.gz'
    postprocess: "dm6.gtf_postprocess"
    conversions:
      - intergenic
      - dexseq
      - astalavista

  fasta:
    url: 'ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/dmel-all-chromosome-r6.11.fasta.gz'
    postprocess: "dm6.fasta_postprocess"
    indexes:
      - bowtie2
      - hisat2
      # - star
  transcriptome:
    url: 'ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/dmel-all-transcript-r6.11.fasta.gz'
    indexes:
      - kallisto

hg19:
  fasta:
    url: 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz'

ecoli:
  fasta:
    url: 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz'
    indexes:
        - bowtie2

wolbachia:
    fasta:
        url: 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000008025.1_ASM802v1/GCF_000008025.1_ASM802v1_genomic.fna.gz'
        indexes:
            - bowtie2
<commit_msg>update references_config.yaml to reflect format changes<commit_after>data_dir: /data/LCDB/references
references:

  -
    assembly: 'dm6'
    type: 'gtf'
    url: 'ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gtf/dmel-all-r6.11.gtf.gz'
    postprocess: "dm6.gtf_postprocess"
    tag: 'r6-11'
    conversions:
      - 'intergenic'

  -
    assembly: 'dm6'
    url: 'ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/dmel-all-chromosome-r6.11.fasta.gz'
    postprocess: "dm6.fasta_postprocess"
    type: 'fasta'
    indexes:
      - 'bowtie2'
      - 'hisat2'

  -
    assembly: 'dm6'
    type: 'fasta'
    tag: 'r6-11_transcriptome'
    url: 'ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/dmel-all-transcript-r6.11.fasta.gz'
    indexes:
      - 'kallisto'

  -
    assembly: 'hg19'
    type: 'fasta'
    url: 'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz'
    indexes:
      - 'bowtie2'
      - 'hisat2'
  -
    assembly: 'hg19'
    type: 'gtf'
    url: 'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz'
    tag: 'gencode-v19'

  -
    assembly: 'hg19'
    type: 'fasta'
    tag: 'gencode_v19_transcriptome'
    url: 'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.pc_transcripts.fa.gz'
    indexes:
      - 'kallisto'

  -
    assembly: 'ecoli'
    type: 'fasta'
    url: 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz'
    indexes:
      - 'bowtie2'

  -
    assembly: 'wolbachia'
    type: 'fasta'
    url: 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000008025.1_ASM802v1/GCF_000008025.1_ASM802v1_genomic.fna.gz'
    indexes:
      - 'bowtie2'

{'fraction_non_alphanumeric': 0.1446164672765658, 'fraction_numerical': 0.06403940886699508, 'mean_word_length': 2.7856191744340877, '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': 1, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2640284', 'n_tokens_mistral': 1398, 'n_tokens_neox': 1216, 'n_words': 124}