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Add "--start" and "--end" arguments to newreference.py to allow for creating subgenic trees #58

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Add "--start" and "--end" arguments to newreference.py to allow for creating subgenic trees #58

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@j23414 j23414 commented Mar 19, 2024

Description of proposed changes

Adds optional "--start" and "--end" arguments to provide 0-based start and end positions respective to a "--gene" of interest.

Since the GenBank sequences can contain extra sequences off the end of the polyprotein, the start and end positions are relative to the gene of interest which was deemed more stable behavior.

Example of only pulling out E gene in Dengue (original)

python scripts/newreference.py \
  --reference dengue_reference.gb \
  --output-fasta E.fasta \
  --output-genbank E.gb \
  --gene E

Will generate a reference genbank with features:

FEATURES             Location/Qualifiers
     CDS             1..1485
                     /gene="E"
                     /product="envelope protein E"
                     /protein_id="NP_740317.1"
     source          1..1485
                     /clone="rDEN4"
                     /db_xref="taxon:11070"
                     /mol_type="genomic RNA"
                     /organism="Dengue virus 4"

Example of pulling E subgenic region (New Feature)

Run with new start and end region:

python scripts/newreference.py \
  --reference dengue_reference.gb \
  --output-fasta E.fasta \
  --output-genbank E.gb \
  --gene E \
  --start 0 \
  --end 9

Will result in:

LOCUS       DENV4/NA/REFERENCE/2003    9 bp    DNA              UNK 01-JAN-1980
DEFINITION  Dengue virus 4, complete genome.
ACCESSION   NC_002640
VERSION     NC_002640.1
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     source          1..9
                     /clone="rDEN4"
                     /db_xref="taxon:11070"
                     /mol_type="genomic RNA"
                     /organism="Dengue virus 4"
     CDS             1..9
                     /gene="E_0_9"
ORIGIN
        1 atgcgatgc
//

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@j23414
Add start and end flags to newreference.py to allow for creating subg…
13ce1a9 
…enic phylogenetic trees

Adds "--start" and "--end" arguments to provide 0-based start and end positions
respective to a "--gene" of interest.

Since the GenBank sequences can contain extra sequences off the end of the polyprotein,
a the start and end positions are relative to the gene of interest was deemed more stable.
@j23414 j23414 linked an issue Mar 19, 2024 that may be closed by this pull request
Add --start and --end flags to newreferences.py to allow for creating subgenic tree builds #56
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@rneher rneher Awaiting requested review from rneher

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Add --start and --end flags to newreferences.py to allow for creating subgenic tree builds
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