process
ensembl.io.genomio.fasta.process
¶
Takes a FASTA file (DNA or peptide), cleans it up and optionally excludes some IDs.
exclude_seq_regions = []
module-attribute
¶
FastaParserError
¶
Bases: Exception
Error while parsing a FASTA file.
Source code in src/python/ensembl/io/genomio/fasta/process.py
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get_peptides_to_exclude(genbank_path, seqr_to_exclude)
¶
Extract peptide IDs from a genbank file that are in a given list of seq regions
Source code in src/python/ensembl/io/genomio/fasta/process.py
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main()
¶
Module's entry-point.
Source code in src/python/ensembl/io/genomio/fasta/process.py
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prep_fasta_data(fasta_infile, genbank_infile, fasta_outfile, peptide_mode=False)
¶
Parameters:
Name | Type | Description | Default |
---|---|---|---|
fasta_file
|
Input FASTA file - DNA / Protein |
required | |
genbank_infile
|
Optional[PathLike]
|
Input GenBank GBFF file (Optional) |
required |
fasta_outfile
|
PathLike
|
Output FASTA sequence file. |
required |
peptide_mode
|
bool
|
Process proteins instead of DNA |
False
|
Source code in src/python/ensembl/io/genomio/fasta/process.py
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