BP_SREFORMAT(1p)

💖 BP_SREFORMAT 💖

okay bestie, welcome to bpsreformat — it's the lil script from the User Contributed Perl Documentation corner of the world, and it's here to do exactly one iconic thing: flip your sequence formats around. 🦋

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✨ NAME ✨

bpsreformat — convert sequence formats, no cap 💅

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🌸 DESCRIPTION 🌸

so this script rides on the SeqIO system, which is the whole reason it can convert sequence formats — and it does it for either straight-up sequence data or multiple sequence alignment data. both. she contains multitudes. 🫶

about the name, because I know you're gonna ask: Sean Eddy's program sreformat (it lives inside the HMMER pkg) already does this exact thing, so the name is a little homage moment. but here's the difference, and it's giving opposite energy: Sean's program tries to guess your input formats, while our code currently makes you say out loud what the input and output formats are, and whether the data is coming from a multiple sequence alignment or from straight sequence files. no guessing, just vibes and explicit flags. 😌

🎀 Usage

bpsreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT

🌈 the options, bestie

• -h/--help — print this help. she's helpful like that 💖
• -if/--informat — specify the input format. tell her what you're feeding her 🍓
• -of/--outformat — specify the output format. tell her what you want back ✨
• -i/--input — specify the input file name. (to pass in data on STDIN use the minus sign as the filename — yes, just -, iconic)
• -o/--output — specify the output file name. (to pass data out on STDOUT use the minus sign as the filename — - again, she's consistent)
• --msa — specify this is multiple sequence alignment data 👑
• --special — will pass on special parameters to the AlignIO/SeqIO object. most of these are for Bio::AlignIO objects, fyi. it takes a comma separated list of the following:
  • nointerleaved — for phylip, non-interleaved format
  • idlinebreak — for phylip, makes it molphy format
  • percentages — for clustalw, show % id per line

lowkey important: with --special you're handing parameters straight to those objects, so keep the list comma-separated and spell them exactly like above. no typos, bestie 🙈

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that's the whole page, and honestly? she ate. this was written for perl v5.32.1, dated 2021-08-15 — so if you're reading this in the future, hi, love that for you, the flags are still the flags. 🎀✨ bye bestie, go convert something 💜