CSV2MIPE(1)

📦
version 1.1 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 CSV2MIPE(1) — the csv2mipe.pl glow-up 💖

okay bestie, gather round, because this little script is literally the moment. csv2mipe.pl takes your messy lil tab-delimited files and generates a MIPE file out of them — and yes, it's based on MIPE version v1.1, no cap. 🦋

So it eats 3 tab-delimited files, and here's the whole menu:

  • a tab-delimited file with PCR-level data
  • a tab-delimited file with SNP-level data
  • a tab-delimited file with assay-level data

🌸 NAME 🌸

csv2mipe.pl — generates a MIPE file based on 3 tab-delimited files, based on MIPE version v1.1. 👑

✨ the PCR-level data file — here's what columns it needs ✨

Not me being so specific about this, but every one of these has to be there:

  • pcr_id
  • pcr_modified (might be multiple, divided by semi-colon ";")
  • pcr_project (might be multiple, divided by semi-colon ";")
  • pcr_researcher (might be multiple, divided by semi-colon ";")
  • pcr_species
  • source_type
  • source_id
  • design_seq
  • primer1_oligo
  • primer1_seq
  • primer1_tm
  • primer2_oligo
  • primer2_seq
  • primer2_tm
  • design_remark (might be multiple, divided by semi-colon ";")
  • use_seq
  • use_revcomp
  • use_remark (might be multiple, divided by semi-colon ";")
  • pcr_remark (might be multiple, divided by semi-colon ";")

🎀 the SNP-level data file — columns go here 🎀

  • pcr_id
  • snp_id
  • snp_pos
  • snp_amb
  • snp_remark (might be multiple, divided by semi-colon ";")

💜 the assay-level data file — columns, but make it assay 💜

  • pcr_id
  • snp_id
  • assay_id
  • assay_type
  • assay_enzyme
  • assay_oligo
  • assay_specific
  • assay_tail
  • assay_strand
  • assay_remark (might be multiple, divided by semi-colon ";")

✨ SYNOPSIS ✨

the way you just run it, three files, in order, that's it, periodt:

csv2mipe.pl <pcr_file.csv> <snp_file.csv> <assay_file.csv>

🌈 ADDITIONAL INFO 🌈

lowkey iconic extra reading, go check it:

👑 AUTHOR 👑

  • Jan Aerts (jan.aerts@bbsrc.ac.uk)

and that's the whole vibe, bestie 🫶 this was brought to you by perl v5.32.1, dated 2021-02-21, serving CSV2MIPE(1) realness 💅✨

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