Recent Releases of fasta-rbca-resolver
fasta-rbca-resolver -
To assign standardized country names from geographic metadata embedded in FASTA headers, this study implemented a deterministic matching strategy known as the Rule-Based Country Assignment (RBCA). First, HA protein sequences in FASTA format were parsed using Biopython v1.81, extracting only the "Name" field from each record. Virus names followed the GISAID-recommended structure: A/host/location/isolate/year. A custom regular expression parser was applied to isolate the third component—assumed to represent the sampling location—which was then tabulated and saved in locationlist.csv. In the next step, these extracted location names were matched exactly against a custom JSON dictionary (locationtocountryISO31661.json) containing only ISO 3166-1 short English country names. No aliases, abbreviations, or user-defined variants were included. The processing script Fasta-rbca R1.ipynb exclusively relied on this dictionary for precise lookup. Locations that failed to match were labeled as "Other" and retained alongside successful assignments for completeness. All results were consolidated and exported to country_stat.csv, ensuring traceable, reproducible mapping.
- Jupyter Notebook
Published by Bambusaoldhamii 10 months ago
fasta-rbca-resolver -
To assign standardized country names from geographic metadata embedded in FASTA headers, this study implemented a deterministic matching strategy known as the Rule-Based Country Assignment (RBCA). First, HA protein sequences in FASTA format were parsed using Biopython v1.81, extracting only the "Name" field from each record. Virus names followed the GISAID-recommended structure: A/host/location/isolate/year. A custom regular expression parser was applied to isolate the third component—assumed to represent the sampling location—which was then tabulated and saved in locationlist.csv. In the next step, these extracted location names were matched exactly against a custom JSON dictionary (locationtocountryISO31661.json) containing only ISO 3166-1 short English country names. No aliases, abbreviations, or user-defined variants were included. The processing script Fasta-rbca R1.ipynb exclusively relied on this dictionary for precise lookup. Locations that failed to match were labeled as "Other" and retained alongside successful assignments for completeness. All results were consolidated and exported to country_stat.csv, ensuring traceable, reproducible mapping.
- Jupyter Notebook
Published by Bambusaoldhamii 10 months ago