GM2SEGS(1)

💖 GM2SEGS 💖

okay bestie, welcome to gm2segs — straight out of the NCBI Entrez Direct User's Manual, section 1 (that's your general commands era ✨). this is the little glow-up tool that takes GeneMachine BLAST alignments and turns them into a tidy coordinate table. no cap, it's giving "I just want the numbers, please" 💅

✨ NAME ✨

gm2segs — present GeneMachine BLAST alignments in tabular form 🦋

🌸 SYNOPSIS 🌸

gm2segs [-0-based|-zero-based|-1-based|-one-based|-ucsc-based]

like... that's it. one optional flag situation. pick your coordinate vibe and go 👑

🎀 DESCRIPTION 🎀

so here's the tea ☕: gm2segs reads BLAST alignments from GeneMachine off standard input, and writes a sorted table of their hits' coordinates to standard output. it's a glow-up pipeline moment — messy alignments in, clean little table out 💖

fr fr, stdin in, stdout out. that's the whole main character arc.

💅 OPTIONS 💅

• -0-based, -zero-based — report closed intervals in zero-based coordinates. so like, coordinates that start counting at 0, and both ends are included 🍓
• -1-based, -one-based — report closed intervals in one-based coordinates. this is the default, bestie, so if you don't say anything, this is what you get 🌈
• -ucsc-based — report half-open intervals in zero-based coordinates. yes, the UCSC situation: start is zero-based, end is exclusive 🧚

not me stressing the difference between closed and half-open — it literally changes the numbers, so pick carefully 🔥

⭐ SEE ALSO ⭐

• xtract(1) — go peek at that one too, iykyk 💜

and that's the whole page, bestie 🫶 this lil' icon lives in the NCBI Entrez Direct User's Manual, and this version was cooked up on 2025-05-26 — shoutout to NCBI for keeping the lights on ✨ mwah, slay, periodt 💖