gm2segs

name	gm2segs
description	Use when converting BLASTN mRNA alignment XML into segmented interval reports and strand-overlap summaries in EDirect pipelines.
disable-model-invocation	true
user-invocable	true

gm2segs

CLI tool from the Entrez Direct (EDirect) suite that processes genomic map data and converts it to segment intervals. Reports counts for raw (RAW), plus strand (PLS), minus strand (MNS), and combined (CMB) intervals, detecting overlaps where both strands share coordinates.

Quick Start

• Command: PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/gm2segs -1-based < alignments.xml
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gm2segs
• Full reference: See references/help.md for detailed documentation

When To Use This Tool

• Converting genomic map input to segmented interval output
• Detecting overlapping intervals between plus and minus strands
• Summarizing interval counts by strand orientation
• Piping output from other EDirect tools like xtract

Common Patterns

# 1) Generate the default 1-based segment report
PATH=/home/vimalinx/miniforge3/envs/bio/bin: \
  /home/vimalinx/miniforge3/envs/bio/bin/gm2segs -1-based \
  < alignments.xml