Gene2range

gene2range

Quick Start

• Command: PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/gene2range chr1 < gene_summaries.xml
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gene2range
• Reference: See references/help.md for detailed usage and examples

When To Use This Tool

• Filter DocumentSummary XML down to one chromosome with normalized Min / Max coordinates.
• Convert Entrez Gene summaries into GENE XML blocks that downstream helpers such as find-in-gene can consume.
• Preserve strand direction by inferring plus or minus from ChrStart versus ChrStop.

Common Patterns

# 1) Convert chr1 gene summaries into sorted GENE XML
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/gene2range chr1 \
  < gene_summaries.xml \
  > chr1_ranges.xml

# 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.