DEFINECLONES.PY(1)

💖 DEFINECLONES.PY(1) 💖

okay bestie, this is the DEFINECLONES.PY(1) page, and it's giving User Commands energy 💅 It's all about DefineClones.py, a toolkit for sorting Ig sequences into clones 🧬✨

✨ NAME ✨

DefineClones.py is a repertoire clonal assignment toolkit written for Python 3 🌸

✨ DESCRIPTION ✨

Here's how you call it 🎀

DefineClones.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}] [--nproc NPROC] [--sf SEQ_FIELD] [--vf V_FIELD]
       [--jf J_FIELD] [--gf GROUP_FIELDS [GROUP_FIELDS ...]]  [--mode
       {allele,gene}] [--act {first,set}] [--model
       {ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat}]
       [--dist DISTANCE] [--norm {len,mut,none}] [--sym {avg,min}]
       [--link {single,average,complete}] [--maxmiss MAX_MISSING]

The main job here is to assign Ig sequences into clones 🦋 It's literally the whole vibe ✨

💅 help:

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

🎀 standard arguments:

• -d DB_FILES [DB_FILES ...] — a list of tab delimited database files. (default: None) 🍓
• -o OUT_FILES [OUT_FILES ...] — an explicit output file name. Heads up, this one can't be used with --failed, --outdir, or --outname. If you don't set it, the output filename gets based on the input filename(s). (default: None) 💜
• --outdir OUT_DIR — changes the output directory to the location you pick. If you skip this, the input file directory gets 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 it with multiple input files. (default: None) ✨
• --log LOG_FILE — writes verbose logging to a file. Also can't be used with multiple input files. (default: None) 📝
• --failed — creates files containing the records that fail processing. (default: False) 💀
• --format {airr,changeo} — sets the input and output format. (default: airr) 🦋
• --nproc NPROC — how many simultaneous computational processes run at once (aka how many CPU cores get used). (default: 8) ⚡

🧬 cloning arguments:

• --sf SEQ_FIELD — the field used to calculate distance between records. It defaults to junction (airr) or JUNCTION (changeo). (default: None) 🫶
• --vf V_FIELD — the field holding the germline V segment call. It defaults to v_call (airr) or V_CALL (changeo). (default: None) 👑
• --jf J_FIELD — the field holding the germline J segment call. It defaults to j_call (airr) or J_CALL (changeo). (default: None) 🌈
• --gf GROUP_FIELDS [GROUP_FIELDS ...] — extra fields for grouping clones, on top of V, J and junction length. (default: None) 🧚
• --mode {allele,gene} — picks whether the initial grouping uses the V(D)J allele or the gene. (default: gene) 🍓
• --act {first,set} — decides how multiple V(D)J assignments get handled for the initial grouping. The "first" action only uses the first gene listed. The "set" action uses all gene assignments and builds a bigger gene grouping made of any sequences that share an assignment or get linked to another sequence by a common assignment (kinda like single-linkage) 🔗 (default: set)
• --model {ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat} — picks the substitution model used to calculate distance between sequences. The "ham" model is nucleotide Hamming distance and "aa" is amino acid Hamming distance. The "hh_s1f" and "hh_s5f" models are human specific single nucleotide and 5-mer content models, respectively, from Yaari et al, 2013. The "mk_rs1nf" and "mk_rs5nf" models are mouse specific single nucleotide and 5-mer content models, respectively, from Cui et al, 2016.

⚠️ The "m1n_compat" and "hs1f_compat" models are deprecated 💀 They only exist for backwards compatibility with the "m1n" and "hs1f" models in Change-O v0.3.3 and SHazaM v0.1.4. And both 5-mer models should be considered experimental 🙈

Default for this one is ham.

• --dist DISTANCE — the distance threshold for clonal grouping. (default: 0.0) 📏
• --norm {len,mut,none} — how distances get normalized. Pick one of none (don't normalize), len (normalize by length), or mut (normalize by the number of mutations between sequences). (default: len) 💫
• --sym {avg,min} — how asymmetric distances get combined. Pick avg (the average of A->B and B->A) or min (the minimum of A->B and B->A). (default: avg) 🦋
• --link {single,average,complete} — the type of linkage used for hierarchical clustering. (default: single) 🌸
• --maxmiss MAX_MISSING — the max number of non-ACGT characters (gaps or Ns) allowed in the junction sequence before the record gets kicked out of clonal assignment.

🚨 Under single linkage, non-informative positions can create artifactual links between unrelated sequences. Use with caution, bestie!

(default: 0)

📂 output files:

• clone-pass — a database with assigned clonal group numbers 🎉
• clone-fail — a database with records that failed clonal grouping 😭

🔑 required fields:

• sequence_id, v_call, j_call, junction 🫶

🏷️ output fields:

• clone_id ✨

✨ AUTHOR ✨

This manpage was written by Nilesh Patra for the Debian distribution 🌈 and it can be used for any other usage of the program. Thank you, Nilesh, you're iconic 💜

Byeee bestie 🦋 this page came from DefineClones.py 1.0.1, dated October 2020, and it's filed under DEFINECLONES.PY(1) 🎀 Stay slay, periodt 💖✨