| name | spdi2tbl |
| description | Use when flattening SPDI XML records into sorted, deduplicated tabular rows for downstream variant pipelines. |
| disable-model-invocation | true |
| user-invocable | true |
spdi2tbl
Tiny Bash wrapper around xtract plus a final sort-table | cut | uniq cleanup. It reads <SPDI> XML, emits variant rows with rsID, accession, position, deleted/inserted sequence, class, type, and gene, then sorts and deduplicates the result.
Quick Start
- Command:
... | spdi2tbl
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/spdi2tbl
- Typical upstream:
efetch -db snp ... | snp2hgvs | hgvs2spdi
When To Use This Tool
- Flattening SPDI XML into plain tabular rows
- Bridging from
hgvs2spdi into shell-friendly TSV output
- Producing deduplicated variant tables for later ranking, filtering, or product-sequence generation
- Normalizing dbSNP-derived variant classes into a stable sort order
Common Patterns
efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2tbl
some_spdi_xml_generator | spdi2tbl > variants.tsv
efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2tbl | tbl2prod
Recommended Workflow
- Generate real
<SPDI> XML upstream, typically from hgvs2spdi.
- Pipe the XML into
spdi2tbl.
- Inspect the resulting 8-column rows before using them downstream.
- Chain into
tbl2prod or other shell filters only after confirming the accession/class mix is what you expect.
Guardrails
- There is no safe local help/version path: both
-h and --version fell through to xtract and failed with No data supplied to xtract from stdin or file.
- Source inspection shows the class ordering is explicitly transformed as
Genomic=1, Coding=2, Protein=3 before sorting.
- The wrapper depends on
sort-table being available on PATH.
- In live testing on rs104894914, the output rows looked like
rs104894914 NC_000023.11 154191715 T C Genomic Substitution OPN1MW.
- Final output is deduplicated with
uniq after sorting, so repeated equivalent rows are collapsed silently.
