tbl2prod

name	tbl2prod
description	Use when converting `spdi2tbl`-style variant rows into reference and altered product sequences for coding or protein variants.
disable-model-invocation	true
user-invocable	true

tbl2prod

Pipeline helper that reads 8-column variant rows of the form rsid accn ofs del ins cls typ gene, fetches the referenced nucleotide or protein record from NCBI, and emits reference/product peptide sequences for non-genomic variants.

Quick Start

• Command: ... | tbl2prod
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/tbl2prod
• Typical upstream: ... | spdi2tbl

When To Use This Tool

• Translating coding or protein variant rows into actual product sequences
• Extending spdi2tbl output with reference and altered peptide strings
• Comparing wild-type and mutated products for rsID-derived non-genomic variants
• Staying inside the EDirect shell-tool chain for sequence/product derivation

Common Patterns

# Full dbSNP-to-product pipeline
efetch -db snp -id 104894914 -format docsum | snp2hgvs | hgvs2spdi | spdi2tbl | tbl2prod

# Feed a prepared spdi2tbl-style table
cat variants.tsv | tbl2prod

# Save the resulting product table
cat variants.tsv | tbl2prod > products.tsv

Recommended Workflow

1. Feed tbl2prod the exact 8-column tabular rows produced by spdi2tbl or an equivalent generator.
2. Expect only coding and protein variants to survive; genomic rows are skipped.
3. Capture the three-column output and compare the reference (:+) and altered (:ins) definitions as needed.
4. Use the result for downstream interpretation, not as a generic annotation-file conversion step.

Guardrails

• The old autogenerated description was wrong: this script does not read NCBI feature-table .tbl files.
• It expects tab-delimited rows shaped like rsid accn ofs del ins cls typ gene; malformed or differently ordered input will misparse silently.
• -h and --version are not implemented; with no stdin they simply produce no useful output.
• Source inspection shows the script skips Genomic rows entirely, fetches sequence records with efetch -format gp, and uses gbf2xml, xtract, and several transmute transforms internally.
• In live testing on rs104894914, the output included both a reference product row such as rs104894914 NM_000513.2:688:T:+ <protein> and an altered product row such as rs104894914 NM_000513.2:688:T:C <protein>.
• The final output is sorted and reduced to three columns via sort-table ... | cut -f 1-2,4.