MIPE2DBSTS(1)

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

💖 MIPE2DBSTS(1) 💖

okay so bestie, welcome to the User Contributed Perl Documentation section, which is basically where the community's fave little scripts live rent-free. today's main character is mipe2dbSTS.pl and she is serving. pull up a chair, grab a boba, and let's get into it. 🧋✨

✨ NAME ✨

mipe2dbSTS.pl — she generates an input file for submission to dbSTS. 💅

what's included in the output, you ask? the STS section of the dbSTS submission, based on MIPE version v1.1. she's a whole era. 👑

the arguments she takes:

  • mipe_file
  • a config file
  • (optional) a list of PCR IDs

🌸 DESCRIPTION 🌸

so the config file? it's literally just lines with a key and a value, separated by an equal sign (=). simple. iconic. no notes. 🎀

the key is made of the lowercase name of the NCBI submission file (peep the dbSTS website, iykyk), then an underscore, then the lowercase name of the field in that file. that's the whole formula, bestie.

the following fields should be defined in the config file:

pub_title=
pub_authors=
source_name=
source_organism=
cont_name=
cont_fax=
cont_tel=
cont_email=
cont_lab=
cont_inst=
cont_addr=
protocol_name=
protocol_protocol=
buffer_name=
buffer_buffer=
sts_pcr_profile=
heads up bestie 🫶 for protocol_protocol, buffer_buffer and sts_pcr_profile, more lines are necessary — peep the example below.

an example of a config file looks like this, and honestly? she ate:

pub_title=Genetic mapping of chicken SNPs
pub_authors=Aerts,J.A.; Veenendaal,T.; Crooijmans,R.P.M.A; Groenen,M.A.M
source_name=Chicken genomic DNA
source_organism=Gallus gallus
cont_name=Jan Aerts
cont_fax=+31 317 483929
cont_tel=+31 317 483397
cont_email=jan.aerts@wur.nl
cont_lab=Animal Breeding and Genomics Group
cont_inst=Wageningen University
cont_addr=PO Box 338, 6700 AH Wageningen, The Netherlands
protocol_name=Protocol_Aerts
protocol_protocol=Template:    30-60 ng
protocol_protocol=Primer:     each 4 uM
protocol_protocol=dNTPs:    each 200 uM
protocol_protocol=Taq:        0.3 units
protocol_protocol=Volume:         12 ul
buffer_name=Buffer_Aerts
buffer_buffer=MgCl2:         1.5 mM
buffer_buffer=(NH4)2SO4:      20 mM
buffer_buffer=Tris-HCl:       75 mM
buffer_buffer=Tween 20: 0.01% (w/v)
buffer_buffer=pH:               8.8

💀 BUGS 💀

Unknown. like, she's been unproblematic so far fr fr. but if you do encounter one, please let her know at jan.aerts@wur.nl. she wants the tea. ☕🙈

🌈 SYNOPSIS 🌈

mipe2dbSTS.pl your_file.mipe dbSTS.config <pcr_id1> <pcr_id2>

that's it. that's the whole vibe check. ✨

🦋 ADDITIONAL INFO 🦋

see http://mipe.sourceforge.net for more. go look, it's giving resources. 📚💜

👑 AUTHOR 👑

Jan Aerts (jan.aerts@bbsrc.ac.uk) — the legend herself. we stan. 🌟

and that's the whole page bestie!! this one's running on perl v5.32.1, dated 2021-02-21, and it lives in the MIPE2DBSTS(1) section. go forth and submit those STSs. slay, periodt. 💅🎀✨🫶

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