MAKEDB.PY(1)

📦 version 1.3.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 Hiii bestie, welcome to the MakeDb.py manual, aka the MAKEDB.PY(1) page 🦋

✨ NAME ✨

MakeDb.py - Repertoire clonal assignment toolkit (Python 3) 🧬

🌸 DESCRIPTION 🌸

Okay so here's the vibe: this is the thing that makes a tab-delimited database file to store your sequence alignment info. Literally the main character of the whole workflow 👑

The usage line looks like this:

usage: MakeDb.py [--version] [-h]  ...

🎀 help: 🎀

  • --version — flexes the program's version number and then bounces (exits) 💅
  • -h, --help — shows the help message and exits, no cap 🫶

🧚 subcommands: 🧚

Pick your aligner, bestie. This is the aligner used part of the menu 🔥

  • igblast — processes igblastn output 🌈
  • igblast-aa — processes igblastp output 💜
  • imgt — processes IMGT/HighV-Quest output 🍓
Warning: imgt does not work with V-QUEST. Don't be the girlie who tries it anyway 💀
  • ihmm — processes iHMMune-Align output ✨

🦋 output files: 🦋

  • db-pass — this is the slay pile 💖. It's a database of alignment records with functionality information, V and J calls, and a junction region.
  • db-fail — this is the pile that got rejected 🙈. It's a database of records that fail because of no productivity information, no gene V assignment, no J assignment, or no junction region.

💅 universal output fields: 💅

These fields show up no matter which aligner you pick, so they're the core girl power of the output 👑

sequence_id, sequence, sequence_alignment, germline_alignment,
rev_comp, productive, stop_codon, vj_in_frame, locus, v_call,
d_call, j_call, junction, junction_length, junction_aa,
v_sequence_start, v_sequence_end, v_germline_start,
v_germline_end, d_sequence_start, d_sequence_end,
d_germline_start, d_germline_end, j_sequence_start,
j_sequence_end, j_germline_start, j_germline_end, np1_length,
np2_length, fwr1, fwr2, fwr3, fwr4, cdr1, cdr2, cdr3

🌈 imgt specific output fields: 🌈

These only show up when you're using imgt 🍓

n1_length, n2_length, p3v_length, p5d_length, p3d_length,
p5j_length, d_frame, v_score, v_identity, d_score, d_identity,
j_score, j_identity

🔥 igblast specific output fields: 🔥

These only show up with igblast 💜

v_score, v_identity, v_support, v_cigar, d_score, d_identity,
d_support, d_cigar, j_score, j_identity, j_support, j_cigar

✨ ihmm specific output fields: ✨

These only show up with ihmm 🧚

vdj_score

💖 10X specific output fields: 💖

Only for the 10X crew 🫧

cell_id, c_call, consensus_count, umi_count, v_call_10x,
d_call_10x, j_call_10x, junction_10x, junction_10x_aa

🫶 AUTHOR 🫶

Nilesh Patra wrote this manpage for the Debian distribution, and it can be used for any other usage of the program 🎀

Okay that's the tea 🫖💅 MakeDb.py 1.0.1, October 2020, MAKEDB.PY(1). Byeee bestie, go make those databases 🦋💖

📦 where this page comes from