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:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/gm2segs -1-based \
  < alignments.xml

# 2) Emit UCSC-style coordinates instead
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/gm2segs -ucsc-based \
  < alignments.xml

Recommended Workflow

1. Prepare input data from prior EDirect pipeline steps (e.g., via xtract)
2. Pipe data to gm2segs through stdin
3. Review the output interval counts for each category (RAW, PLS, MNS, CMB)
4. Use reported overlap information to identify strand conflicts or features

Guardrails

• The script depends on several sibling EDirect helpers: xtract, print-columns, sort-table, and fuse-segments must all be on PATH.
• It specifically filters for alignments whose label string equals BLASTN - mrna.
• Output is a multi-section report (RAW, PLS, MNS, CMB), not one flat table.
• Because it reuses fuse-segments, empty strand partitions can still produce the bogus sentinel row 0\t0\t1; interpret MNS / PLS sections cautiously when one strand is absent.