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Adapt to new DH template #184

Merged
merged 79 commits into from
Oct 25, 2024
Merged

Adapt to new DH template #184

merged 79 commits into from
Oct 25, 2024

Commits on Apr 29, 2024

  1. make JSON file required in vcf2gvf.py

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    miseminger committed Apr 29, 2024
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  2. add new attribute, 'transcript_id', using locus_tag from JSON

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    miseminger committed Apr 29, 2024
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  3. add transcript_id in parentheses for HGVS nt names

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    miseminger committed Apr 29, 2024
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  4. get rid of UserWarning for match groups

    @miseminger
    miseminger committed Apr 29, 2024
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  5. remove unused imports

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    miseminger committed Apr 29, 2024
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  6. include alias_protein_id in HGVS alias names, and make a new attribut… 

    …e called 'alias_protein_id'
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  7. update nt_delins_regex

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    miseminger committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. add new attribute, 'gene_symbol', from 'gene' in the JSON file

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  2. add 'gene_symbol' and 'protein_symbol' columns to mutation index

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    miseminger committed Apr 30, 2024
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  3. rename 'gene' column in mutation index to 'gene_name'

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  4. change 'protein symbol' column name to 'gene name' to match GVF and m… 

    …utation index; remove need for JSON file
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  5. change 'protein symbol' column in df made from Pokay repo to 'gene na… 

    …me' to allow merge with mutation index
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Commits on Jul 30, 2024

  1. change 'gene' attribute to 'gene_name' in VCF

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  2. change 'gene' to 'gene_name' and add 'gene_symbol'

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    miseminger committed Jul 30, 2024
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  3. make all args required for log and index creation

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    miseminger committed Jul 30, 2024
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  4. update column names to match DH template, make mutation index optional

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    miseminger committed Jul 30, 2024
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  5. fix formatting for non-index file

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    miseminger committed Jul 30, 2024
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  6. merge dfs on 'protein symbol' instead

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  7. sort by nucleotide position

    @miseminger
    miseminger committed Jul 30, 2024
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  8. update for new functional annotation format

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    miseminger committed Jul 30, 2024
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  9. update to match new functional annotation format

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    miseminger committed Jul 30, 2024
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  10. rename 'alias_protein' to 'mat_pep'

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    miseminger committed Jul 30, 2024
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Commits on Aug 8, 2024

  1. add Pokay names as 'pokay_id'

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    miseminger committed Aug 8, 2024
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  2. add missing 'pokay_id' for ORF8

    @miseminger
    miseminger committed Aug 8, 2024
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Commits on Sep 15, 2024

  1. Add script

    @miseminger
    miseminger committed Sep 15, 2024
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  2. Add SARS-CoV-2 ontology terms JSONs

    @miseminger
    miseminger committed Sep 15, 2024
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  3. Delete unwanted files

    @miseminger
    miseminger committed Sep 15, 2024
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Commits on Sep 16, 2024

  1. upload script

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    miseminger committed Sep 16, 2024
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  2. update comment

    @miseminger
    miseminger committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. Add ontology terms to JSON, and remove pokay_id

    @miseminger
    miseminger committed Sep 17, 2024
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  2. add aliases from Sept 9 issue

    @miseminger
    miseminger committed Sep 17, 2024
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  3. remove alias names that are the same as the gene name

    @miseminger
    miseminger committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. Temporarily add Pokay name for PLpro to aliases

    @miseminger
    miseminger committed Sep 18, 2024
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  2. Add RdRp back in to alias list

    @miseminger
    miseminger committed Sep 18, 2024
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  3. Add protein_alias lists manually

    @miseminger
    miseminger committed Sep 18, 2024
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  4. Add ontology terms to functional annotation file

    @miseminger
    miseminger committed Sep 18, 2024
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  5. Update column names to match template

    @miseminger
    miseminger committed Sep 18, 2024
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  6. Don't merge on mat_pep anymore

    @miseminger
    miseminger committed Sep 18, 2024
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  7. add BioRegistry prefix for doi

    @miseminger
    miseminger committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. Add MPOX ROBOT table

    @miseminger
    miseminger committed Sep 19, 2024
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Commits on Sep 27, 2024

  1. update for MPOX

    @miseminger
    miseminger committed Sep 27, 2024
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  2. Add ontology term JSONs for MPOX

    @miseminger
    miseminger committed Sep 27, 2024
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Commits on Oct 1, 2024

  1. Add strand orientation for MPOX

    @miseminger
    miseminger committed Oct 1, 2024
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  2. add gene and strand orientation for MPOX

    @miseminger
    miseminger committed Oct 1, 2024
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  3. make code useful for SC2 or MPOX

    @miseminger
    miseminger committed Oct 1, 2024
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  4. Update SARS-CoV-2 JSONs with gene and strand orientations:

    @miseminger
    miseminger committed Oct 1, 2024
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  5. Add gene and strand orientation

    @miseminger
    miseminger committed Oct 1, 2024
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  6. Add new functional annotation file

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    miseminger committed Oct 1, 2024
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Commits on Oct 4, 2024

  1. add gene and strand orientation for MPOX, and change unknown publicat… 

    …ion status from 'false' to empty string
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    miseminger committed Oct 4, 2024
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  2. add MPOX functional annotations in DH template format

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    miseminger committed Oct 4, 2024
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Commits on Oct 22, 2024

  1. remove mutation index rows that don't have a nucleotide mutation

    @miseminger
    miseminger committed Oct 22, 2024
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  2. use pd.explode() in unnest_multi()

    @miseminger
    miseminger committed Oct 22, 2024
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  3. workaround unmatched list lengths to work with pd.explode()

    @miseminger
    miseminger committed Oct 22, 2024
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Commits on Oct 23, 2024

  1. Adapt vcf2gvf to new JSON keys

    @miseminger
    miseminger committed Oct 23, 2024
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Commits on Oct 24, 2024

  1. align attribute keys with DH template

    @miseminger
    miseminger committed Oct 24, 2024
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  2. align attribute keys with DH template

    @miseminger
    miseminger committed Oct 24, 2024
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  3. adapt to new JSON keys

    @miseminger
    miseminger committed Oct 24, 2024
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  4. archive copy of gvf2tsv.py

    @miseminger
    miseminger committed Oct 24, 2024
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  5. Produce 1 TSV from GVF, ignoring clades

    @miseminger
    miseminger committed Oct 24, 2024
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  6. Update to match new GVF keys

    @miseminger
    miseminger committed Oct 24, 2024
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  7. add gene_orientation and strand_orientation to gvf

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    miseminger committed Oct 24, 2024
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  8. change VP37 to be alias of OPG057 protein, and add to JSON

    @miseminger
    miseminger committed Oct 24, 2024
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  9. remove VP37 mentions from MPXVgp025

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    miseminger committed Oct 24, 2024
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  10. add protein_alias key to all CDS entries

    @miseminger
    miseminger committed Oct 24, 2024
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  11. add indent to fix bug

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    miseminger committed Oct 24, 2024
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  12. replace 'pokay' with 'template' for generalizability

    @miseminger
    miseminger committed Oct 24, 2024
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  13. Rename functional annotation script

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    miseminger committed Oct 24, 2024
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  14. take 'doi:' off saved dois

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    miseminger committed Oct 24, 2024
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Commits on Oct 25, 2024

  1. add definitely the latest version

    @miseminger
    miseminger committed Oct 25, 2024
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  2. match new DH format

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    miseminger committed Oct 25, 2024
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  3. Delete assets/virus_functionalAnnotation/NC_045512.2/Pokay_functional… 

    …Annotation_SARSCoV2_v1.0.tsv
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  4. Delete assets/virus_functionalAnnotation/NC_045512.2/Pokay_functional… 

    …Annotation_SARSCoV2_v2.0.tsv
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  5. add 'clade' argument and attribute

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    miseminger committed Oct 25, 2024
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  6. Merge branch 'madeline-1' of github.com:cidgoh/nf-ncov-voc into madel… 

    …ine-1
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  7. add 'functional_annotation_resource' attribute

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    miseminger committed Oct 25, 2024
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  8. add functional annotation columns as GVF attributes

    @miseminger
    miseminger committed Oct 25, 2024
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  9. change 'measured_variant_functional_effect_description' attribute to … 

    …'variant_functional_effect_description'
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    miseminger committed Oct 25, 2024
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  10. adapt to new DH template format

    @miseminger
    miseminger committed Oct 25, 2024
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  11. update column names

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    miseminger committed Oct 25, 2024
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