CONVERTDB.PY(1)

💖 CONVERTDB.PY(1) 💖

User Commands vibes, bestie 🎀 Here's the whole manual, no skipping.

✨ NAME ✨

ConvertDb.py - Repertoire clonal assignment toolkit (Python 3) 💅

📖 DESCRIPTION 📖

Here's the usage line, verbatim:

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

Okay so this tool parses tab delimited database files 🧚 It's giving organized data energy.

🎀 help 🎀

• --version — flexes the program's version number, then exits 👋
• -h, --help — pulls up the help message, then exits 🧚

🌈 subcommands 🌈

Everything here is Database operation 💜

• airr — turns your input into an AIRR TSV file 🦋
• changeo — turns your input into a Change-O TSV file 🍓
• fasta — makes a fasta file from your database records ✨
• baseline — makes a specially formatted fasta file from database records for input into the BASELINe website 🔥 The format groups clonally related sequences together, one after another. The germline sequence sits before each clone, and it's marked with headers starting with ">>". Main character formatting 👑
• genbank — makes files for GenBank/TLS submissions 🌸

🦋 output files 🦋

• airr — AIRR formatted database files 💖
• changeo — Change-O formatted database files 💖
• sequences — FASTA formatted sequences output from the subcommands fasta and clip 🧚
• genbank — feature tables and fasta files containing MiAIRR compliant input for tbl2asn 🫶

💜 required fields 💜

These fields are required, so don't skip them 🙈

sequence_id, sequence, sequence_alignment, junction, v_call,
d_call, j_call, v_germline_start, v_germline_end,
v_sequence_start, v_sequence_end, d_sequence_start,
d_sequence_end, j_sequence_start, j_sequence_end

🌸 optional fields 🌸

These ones are optional, so you can skip them if you want 🍓

germline_alignment, c_call, clone_id

🫶 AUTHOR 🫶

Big shoutout to Nilesh Patra, who wrote this manpage for the Debian distribution 👑 You can use it for any other usage of the program too 🌈

Okay bestie, that's the whole tea ☕💅 ConvertDb.py 1.0.1, October 2020, CONVERTDB.PY(1) is the full receipt, so stay iconic 🦋✨