fakit v0.1.6 with new command `replace`

add subcommand replace

Usage

replace name/sequence/by regular expression.

Note that the replacement supports capture variables.
e.g. $1 represents the text of the first submatch.
ATTENTION: use SINGLE quote NOT double quotes in *nix OS.

Examples: Adding space to all bases.

    fakit replace -p "(.)" -r '$1 ' -s

Or use the \ escape character.

    fakit replace -p "(.)" -r "\$1 " -s

more on: http://shenwei356.github.io/fakit/usage/#replace

Usage:
  fakit replace [flags]

Flags:
  -s, --by-seq               replace seq
  -i, --ignore-case          ignore case
  -p, --pattern string       search regular expression
  -r, --replacement string   replacement. supporting capture variables.  e.g. $1 represents the text of the first submatch. ATTENTION: use SINGLE quote NOT double quotes in *nix OS or use the \ escape character.

Examples

1. Remove descriptions

   $ echo -e ">seq1 abc-123\nACGT-ACGT" | fakit replace -p " .+"
   >seq1
   ACGT-ACGT
   

2. Replace "-" with "="

   $ echo -e ">seq1 abc-123\nACGT-ACGT" | fakit replace -p "\-" -r '='
   >seq1 abc=123
   ACGT-ACGT
   

3. Remove gaps in sequences.

   $ echo -e ">seq1 abc-123\nACGT-ACGT" | fakit replace -p " |-" -s
   >seq1 abc-123
   ACGTACGT
   

4. Add space to every base. *ATTENTION: use SINGLE quote NOT double quotes in nix OS

   $ echo -e ">seq1 abc-123\nACGT-ACGT" | fakit replace -p "(.)" -r '$1 ' -s
   >seq1 abc-123
   A C G T - A C G T
   

5. Transpose sequence with csvtk

   $ echo -e ">seq1\nACTGACGT\n>seq2\nactgccgt" | fakit replace -p "(.)" -r  "\$1 " -s | fakit seq -s -u | csvtk space2tab | csvtk -t transpose
   A       A
   C       C
   T       T
   G       G
   A       C
   C       C
   G       G
   T       T