CONVERT_COORDS(1)

📦 version 1.8, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

convert_coords — it converts coordinates of features in a GFF file according to a multiple alignment ✨

(also hi bestie, this lives in the User Commands section of the manual, section 1, iykyk 🫶)

🌸 DESCRIPTION 🌸

Okay so picture this: you've got features sitting in a GFF file, and you've got a multiple alignment, and their coordinate systems are not speaking the same language. That's where this icon comes in. convert_coords converts coordinates of features in a GFF file according to a multiple alignment. 💅

It will map from the coordinate system of any sequence to any other sequence. It can also map to or from the coordinate system of the entire alignment as a whole. And on top of all that?? It supports translation of coordinates by a specified offset. Versatile queen behavior, honestly. 👑

✨ OPTIONS ✨

  • -m <msa_fname> — (required) Name of the file in which the alignment is defined. You literally cannot skip this one bestie, it's required. 🎀
  • -f <gff_fname> — (required) Name of the file in which the features are defined (GFF). Also required. No skipping. 🙈
  • -s <src_frame> — Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. The default behavior is to match features with alignment sequences by name (feature by feature). 🌈
  • -d <dest_frame> — Index of destination frame of reference. Default is 0 (whole MSA). 🦋
  • -p <coord_off> — Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. 🍓
  • -n <coord_off> — Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. 🧚
  • -i FASTA|PHYLIP|MPM|SS — Alignment format. Default is to guess format from file contents. 💜
Heads up bestie: -m and -f are both marked (required), so don't come crying to me when it yells at you for leaving them out. 😭

And that's the whole vibe check! This page is convert_coords version 1.4, dated May 2016. Go forth and map those coordinates, you absolute legend. 💖✨🎀

📦 where this page comes from