lh3 / Tabtk

Introduction

Tabtk is a fast and lightweight tool for processing TAB-delimited formats.

Tabtk Examples

• Basic Unix cut (duplicated columns ignored):

    tabtk cut -f 5,1-3,6,6- file.txt
  

• Reorder columns:

    tabtk cut -rf 5,1-3,6 file.txt
  

• Duplicate columns (duplicated columns not ignored with option -r):

    tabtk cut -rf 1,1,1 file.txt
  

• Use both SPACE and TAB as the delimitor:

    tabtk cut -d space -f 1-3 file.txt
  

• Cut a CSV file:

    tabtk cut -d csv -f 2-4 file.csv
  

  Commas can appear in double-quotation marks.

• Print lines in streamed.txt that matching loaded.txt on the first column:

    tabtk isct loaded.txt streamed.txt
  

• Print lines matching the first two columns:

    tabtk isct -1 1,2 loaded.txt streamed.txt
  

• Fixed-width view of a TAB delimited file and truncate long fields to 20

    tabtk view -l 20 tab.txt | less -S
  

  This by default loads 16MB data to RAM, not the whole file.

• Grep a pattern in specified columns:

    tabtk grep -f 2 "^rs[0-9]+" file.vcf
  

• Compute the mean, min and max of a numeric column:

    tabtk num -c 2 file.txt
  

• Compute the standard deviation and quartile:

    tabtk num -Qc2 file.txt