BP_MRTRANS(1p)

🦋 BP_MRTRANS(1p) — bestie's guide to bp_mrtrans 🦋

okay so. this is a page from the User Contributed Perl Documentation section of the manual, and the whole vibe is: you have a protein alignment, you have cDNA, and you want them to match up. let's get into it 💅

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✨ NAME ✨

bp_mrtrans — it implements a transformer of alignments from protein to mrna coordinates. literally a glow-up for your alignment, no cap 🫶

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🌸 SYNOPSIS 🌸

the way you run it is:

Usage:
  bp_mrtrans -i inputfile -o outputfile [-if input format] [-of output format] [-s cDNA sequence database]  [-sf cDNA sequence format] [-h]

that's the whole recipe bestie, -i and -o are the mandatory girlies, everything else in brackets is optional ✨

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💖 DESCRIPTION 💖

so this script will convert a protein alignment back into a cDNA. it's loosely based on Bill Pearson's mrtrans — shoutout to the blueprint, we respect the blueprint 👑

The options are:

• -o filename — the output filename, and if you don't say anything it defaults to STDOUT (so it just yells at your terminal, iconic)
• -of format — output sequence format, as in a multiple sequence alignment. default is phylip
• -i filename — the input filename. REQUIRED — she is not optional, she is the moment, do not skip her 😭
• -if format — input sequence format, as in a multiple sequence alignment. default is clustalw
• -s, --seqdb filename — the cDNA sequence database file
• -sf, --seqformat — the cDNA seq db format (flatfile sequence format)
• -h — this help menu, aka the "bestie help me" button 🙈

ngl -i is required and -o is not — so if you forget -o it just dumps everything to STDOUT. not a bug, just the vibe ✨

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👑 AUTHOR 👑

Jason Stajich, jason-at-bioperl-dot-org — the main character who wrote this fr fr 💜

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and that's the page!! 🎀 this was rendered by perl v5.32.1 on 2021-08-15, under the <rainbow>BP_MRTRANS(1p)</rainbow> title in the User Contributed Perl Documentation collection. go transform those alignments bestie, you got this 🦋💖