pod5 inspect reads format to match the needs for pod5 subset about pod5-file-format HOT 3 CLOSED

Hi @Kirk3gaard ,

Thanks for this, we will take a look internally now!

• George

from pod5-file-format.

Temporary fix using R on the summary file from "pod5 inspect reads"

R code

# Load library
library(tidyverse)
# load summary file from pod5 inspect reads
data<-read_csv("summary.csv",skip = 1)
# Create a column with filenames based on sequencing channel and 
# write a csv file with columns for filenames and read_id
data %>%
  mutate(filename=paste0("pod5_out_ch_",channel,".pod5")) %>%
  arrange(channel) %>%
  select(filename,read_id) %>%
  write_csv(file = "file_for_sorting_by_channel.csv",col_names = F)

Pod5 subset command

pod5 subset pod5_original/*pod5 --output channel_subset/ --csv file_for_sorting_by_channel.csv

from pod5-file-format.

Hi @Kirk3gaard

We've updated the documentation around pod5 subset which hopefully incorporates your suggestions. We've specifically added the following section:

https://pod5-file-format.readthedocs.io/en/0.1.11/docs/tools.html#example-subsetting-from-pod5-inspect-reads

Furthermore, pod5 subset will now accept csv or tsv inputs for --summary / --table saving you the csv -> tsv step.

Thank you very much for raising this ticket and bringing this to our attention.

Kind regards,
Rich

from pod5-file-format.