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Use when converting Entrez Gene `DocumentSummary` XML for one chromosome into sorted `GENE` interval XML.
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| name | gene2range |
| description | Use when converting Entrez Gene `DocumentSummary` XML for one chromosome into sorted `GENE` interval XML. |
| disable-model-invocation | true |
| user-invocable | true |
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/gene2range chr1 < gene_summaries.xml/home/vimalinx/miniforge3/envs/bio/bin/gene2rangereferences/help.md for detailed usage and examplesDocumentSummary XML down to one chromosome with normalized Min / Max coordinates.GENE XML blocks that downstream helpers such as find-in-gene can consume.plus or minus from ChrStart versus ChrStop.# 1) Convert chr1 gene summaries into sorted GENE XML
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$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
DocumentSummary XML that still contains GenomicInfoType blocks.GENE XML and inspect a few records for Strand, Min, Max, Id, Name, and Desc.xtract, sort-table, tbl2xml), so absolute-path invocation alone can still fail if the bio / EDirect bin directory is missing from PATH.ChrStart and ChrStop; reversed genomic coordinates are normalized into Min / Max with Strand=minus.