PoonLab/MiCall-Lite

How to with multi-file batch processing

Closed this issue · 4 comments

hihuhu commented

I just used this program, but I am not a computer professional, I now have 10 files, I want to dispose of one time, do not want to dispose of one time, what should I do? I tried to run in many terminals at the same time, but I couldn't. I hope the author can give me some advice.

ArtPoon commented

Hi @hihuhu! There are many ways to do batch processing on the command line, such as writing a bash script, but this is usually too complicated for a new user. I guess the simplest approach would be for me to write a batch script for you to try. Give me a minute.

hihuhu commented

Thank you very much for your help.

ArtPoon commented

Ok, I've posted a new Python script as a GitHub gist, which you can access here.

To run this script, you just need to provide an absolute or relative path to the directory containing the FASTQ gzip-compressed files that you want to process:

art@orolo:~/git/micall/bin$ python3 batch-micall.py /data/miseq/integrase/
Detected 523 gzipped FASTQ files at /data/miseq/integrase/
/data/miseq/integrase/DR-88-13-2_S180_L001_R1_001.fastq.gz
MiCall-Lite running sample DR-88-13-2_S180_L001_R1_001...
  Preliminary map
  Iterative remap
  Generating alignment file
  Generating count files
/data/miseq/integrase/DR-240-16_S305_L001_R1_001.fastq.gz
MiCall-Lite running sample DR-240-16_S305_L001_R1_001...
  Preliminary map
  Iterative remap
hihuhu commented

Thank you！