CREATEGERMLINES.PY(1)

CREATEGERMLINES.PY(1) 🌸 User Commands manual — bestie, this is your tea ☕

✨ NAME ✨

CreateGermlines.py is a Repertoire clonal assignment toolkit (Python 3) 💅

✨ DESCRIPTION ✨

Okay so here's the vibe. You run it like this:

usage: CreateGermlines.py [--version] [-h] -d DB_FILES [DB_FILES ...]
       [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
              [--outname OUT_NAME] [--log LOG_FILE] [--failed] [--format
              {airr,changeo}] -r REFERENCES [REFERENCES ...]  [-g
              {full,dmask,vonly,regions} [{full,dmask,vonly,regions} ...]]
              [--cloned] [--sf SEQ_FIELD] [--vf V_FIELD] [--df D_FIELD] [--jf
              J_FIELD] [--cf CLONE_FIELD]

It reconstructs germline sequences from alignment data 🧬✨ It's giving precision, bestie.

💖 help 💖

• --version — shows the program's version number and then exits 🦋
• -h, --help — shows the help message and exits 🫶

🎀 standard arguments 🎀

• -d DB_FILES [DB_FILES ...] — Give it a list of tab delimited database files 📂 (default: None)
• -o OUT_FILES [OUT_FILES ...] — pick an explicit output file name. Heads up, this one can't be mixed with --failed, --outdir, or --outname 🙅‍♀️ If you skip it, the output filename gets built from your input filename(s) ✨ (default: None)
• --outdir OUT_DIR — switches the output directory to wherever you point it 📁 If you don't, the input file's directory is used 🌈 (default: None)
• --outname OUT_NAME — changes the prefix of the successfully processed output file to whatever string you give it 💜 You can't use this with multiple input files 💀 (default: None)
• --log LOG_FILE — writes verbose logging to a file 📝 Same deal, it can't be used with multiple input files 🙈 (default: None)
• --failed — makes files full of the records that fail processing 💀 (default: False)
• --format {airr,changeo} — sets the input and output format 🍓 (default: airr)

🌸 germline construction arguments 🌸

• -r REFERENCES [REFERENCES ...] — your list of folders and/or fasta files (with .fasta, .fna or .fa extensions) holding the germline sequences 🧚 (default: None)

Lowkey important: when you're using the default Change-O sequence and coordinate fields, those reference sequences must contain IMGT-numbering spacers (gaps) in the V segment 🚨 Alternative numbering schemes, or no numbering at all, may work for alternative sequence and coordinate definitions that make a valid alignment, but you'll get a warning ⚠️

• -g {full,dmask,vonly,regions} [{full,dmask,vonly,regions} ...] — picks which germline type(s) to include: the full germline, the germline with the D segment masked, or the germline for the V segment only 👑 (default: ['dmask'])
• --cloned — creates only one germline per clone 🦋

Ngl, watch out here: if allele calls are ambiguous within a clonal group, this places the germline call used for the entire clone into the germline_v_call, germline_d_call and germline_j_call fields 👀 (default: False)

• --sf SEQ_FIELD — the field containing the aligned sequence. It defaults to sequence_alignment (airr) or SEQUENCE_IMGT (changeo) 💅 (default: None)
• --vf V_FIELD — the field containing the germline V segment call. It defaults to v_call (airr) or V_CALL (changeo) ✨ (default: None)
• --df D_FIELD — the field containing the germline D segment call. It defaults to d_call (airr) or D_CALL (changeo) 🌈 (default: None)
• --jf J_FIELD — the field containing the germline J segment call. It defaults to j_call (airr) or J_CALL (changeo) 🫶 (default: None)
• --cf CLONE_FIELD — the field with clone identifiers. This one gets ignored unless you also specify --cloned 🙄 It defaults to clone_id (airr) or CLONE (changeo) 💖 (default: None)

🦋 output files 🦋

• germ-pass — a database with the assigned germline sequences 🎉
• germ-fail — a database with the records that failed germline assignment 😭

🧚 required fields 🧚

These fields must be there, no excuses 💅

sequence_id, sequence_alignment, v_call, d_call, j_call, 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

🍓 optional fields 🍓

n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length, clone_id

💜 output fields 💜

These are what you get back, periodt 👑

germline_v_call, germline_d_call, germline_j_call, germline_alignment, germline_alignment_d_mask, germline_alignment_v_region, germline_regions,

✨ AUTHOR ✨

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program 🫶

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And that's the whole tea, bestie! 💖 You're now officially a CreateGermlines.py expert, version 1.0.1 from October 2020 🌸✨ Go slay your repertoire 💅👑