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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

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miseminger
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...and some older fixes for HGVS names

@miseminger
make JSON file required in vcf2gvf.py
c37cd21
@miseminger
add new attribute, 'transcript_id', using locus_tag from JSON
9a4f86d
@miseminger
add transcript_id in parentheses for HGVS nt names
407381c
@miseminger
get rid of UserWarning for match groups
ecd19c4
@miseminger
remove unused imports
1a57d85
@miseminger
include alias_protein_id in HGVS alias names, and make a new attribut…
047f085 
…e called 'alias_protein_id'
@miseminger
update nt_delins_regex
e18dfa9
@miseminger
add new attribute, 'gene_symbol', from 'gene' in the JSON file
82f2959
@miseminger
add 'gene_symbol' and 'protein_symbol' columns to mutation index
418c65d
@miseminger
rename 'gene' column in mutation index to 'gene_name'
efcce0c
@miseminger
change 'protein symbol' column name to 'gene name' to match GVF and m…
0b6f5e5 
…utation index; remove need for JSON file
@miseminger
change 'protein symbol' column in df made from Pokay repo to 'gene na…
c93085c 
…me' to allow merge with mutation index
@miseminger
change 'gene' attribute to 'gene_name' in VCF
257d230
@miseminger
change 'gene' to 'gene_name' and add 'gene_symbol'
f998ed3
@miseminger
make all args required for log and index creation
d3174fe
@miseminger
update column names to match DH template, make mutation index optional
0ff0245
@miseminger
fix formatting for non-index file
ed67400
@miseminger
merge dfs on 'protein symbol' instead
28ad84d
@miseminger
sort by nucleotide position
50689b0
@miseminger
update for new functional annotation format
baf3cb0
@miseminger
update to match new functional annotation format
ec976f8
@miseminger
rename 'alias_protein' to 'mat_pep'
bfd06d3
@miseminger
add Pokay names as 'pokay_id'
51b3f94
@miseminger
add missing 'pokay_id' for ORF8
2d72b02
@miseminger
Add script
da12255
@miseminger
Add SARS-CoV-2 ontology terms JSONs
8551053
@miseminger
Delete unwanted files
21d5b6a
@miseminger
upload script
e6592d2
@miseminger
update comment
54bb4ac
@miseminger
Add ontology terms to JSON, and remove pokay_id
8955e30
miseminger
miseminger commented Oct 24, 2024
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#183

miseminger and others added 16 commits October 24, 2024 13:58
@miseminger
add protein_alias key to all CDS entries
977fc0f
@miseminger
add indent to fix bug
179844e
@miseminger
replace 'pokay' with 'template' for generalizability
496ca37
@miseminger
Rename functional annotation script
a214a34
@miseminger
take 'doi:' off saved dois
3ed9712
@miseminger
add definitely the latest version
673ad82
@miseminger
match new DH format
d689609
@miseminger
Delete assets/virus_functionalAnnotation/NC_045512.2/Pokay_functional…
8e68d0c 
…Annotation_SARSCoV2_v1.0.tsv
@miseminger
Delete assets/virus_functionalAnnotation/NC_045512.2/Pokay_functional…
41f8cc5 
…Annotation_SARSCoV2_v2.0.tsv
@miseminger
add 'clade' argument and attribute
4be0584
@miseminger
Merge branch 'madeline-1' of github.com:cidgoh/nf-ncov-voc into madel…
33d97c7 
…ine-1
@miseminger
add 'functional_annotation_resource' attribute
422f97b
@miseminger
add functional annotation columns as GVF attributes
b72ebcc
@miseminger
change 'measured_variant_functional_effect_description' attribute to …
ce13700 
…'variant_functional_effect_description'
@miseminger
adapt to new DH template format
626dae7
@miseminger
update column names
377ad62
This was linked to issues Oct 25, 2024
change "gene" attribute in GVF to "gene_name" #170
Closed
Correct HGVS nucleotide names to be indexed from the start of the reference genome #165
Closed
Pokay parsing #134
Open
Update the HGVS annotation #102
Open
@anwarMZ anwarMZ merged commit 3c5bc08 into development Oct 25, 2024
@miseminger miseminger deleted the madeline-1 branch October 28, 2024 02:17
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@anwarMZ anwarMZ anwarMZ approved these changes

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