Gene2range

# 2) Use directly in a larger Entrez XML pipeline
upstream_gene_summary_command | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/gene2range chr2

Recommended Workflow

1. Start from DocumentSummary XML that still contains GenomicInfoType blocks.
2. Pass the target chromosome name as the sole positional argument.
3. Capture the emitted GENE XML and inspect a few records for Strand, Min, Max, Id, Name, and Desc.
4. Feed that XML into downstream interval helpers only after confirming the chromosome filter behaved as expected.

Guardrails

• The only required positional argument is the chromosome name; the script reads gene summaries from stdin.
• This wrapper depends on sibling EDirect tools (xtract, sort-table, tbl2xml), so absolute-path invocation alone can still fail if the bio / EDirect bin directory is missing from PATH.
• Output is XML, not a plain TSV coordinate table.
• Strand is inferred by comparing ChrStart and ChrStop; reversed genomic coordinates are normalized into Min / Max with Strand=minus.