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cleans up masterlist and aggregates photos, sequences and freezer contents

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PTM Masterlist cleaning

cleans up PTM masterlist and aggregates photos, sequences and freezer contents

Pre-requisites

  • get access to Martone Lab server via Botany IT (photos or sequences) -> or use Martone Lab Computer
  • get access to PTM Master List
  • have R and IDE (ie. Rstudio) installed

Dependencies

run these lines of code in your Console if you use RStudio

install.packages("tidyverse","leaflet","readxl","janitor","googlesheets4") devtools::install_github("martonelab/ptm")

  • 2020 March Note googlesheets4 - write_sheets functionality is not on CRAN yet: devtools::install_github("tidyverse/googlesheets4")

Files

  • 01_metadata_cleaning - standarizes text data and coordinate data
  • 02_integrate_photos - checks the photos on the Martone Lab server and adds the information to the masterlist
  • 03_integrate_sequences - checks the sequences on the Martone Lab server and adds the corresponding information
  • 04_integrate_freezer - updates the Master List based upon the freezer inventory done in January 2020

Usage

  • Note all the code templates saves the files to the output folder and can be run independently
*** BEFORE YOU DO ANYTHING - Save a copy of the masterlist as an xlsx file in the server ***
  • server: martonelab/Lab Operation/masterlist_archive
  • save as: YYYYMMMDD_PTM - Master List.xlsx
  • ie. 2020Mar18_PTM - Master List.xlsx

Use cases:

  1. Clean from top to bottom
  • run code files 01 to 04 in sequence
  1. Update photos or sequences
  • run the corresponding code file (02 or 03)
  • default is to save to the masterlist

PTM Masterlist

  • review columns after the code is run
  • keep the columns after

File Naming

Following these rules will ensure all information gets reflected properly when combined.

Photos

  • PTM[insert number here].jpg
  • no spaces!
  • ie. PTM1234.jpg

Sequences

  • please follow Nanuq guidelines
  • PTM[Number] __ [primername] __ [additional info provided by nanuq]
  • ie. PTM1500_TLF5_P1512217_076.ab1 (underscores)
  • should not be in any additional folders
  • Currently accepted primers: "rbclrevnew", "gwsfn", "gwsrx", "psbar2", "psbaf", "F7553", "f|F57", "R1150K"

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