SeqKit v0.5.4

Changelog

• seqkit subseq --gtf, add flag --gtf-tag to set tag that's outputted as sequence comment
• fix seqkit split and seqkit sample: forget not to wrap sequence and quality in output for FASTQ format
• compile with go1.8.1

SeqKit v0.5.3

Changelog

• seqkit grep: fix bug when using seqkit grep -r -f patternfile:
  all records will be retrived due to failing to discarding the blank pattern (""). #11

SeqKit v0.5.2

Changelog

• seqkit stats -a and seqkit seq -g -G: change default gap letters from '- ' to '- .'

• seqkit subseq: fix bug of range overflow when using -d/--down-stream
  or -u/--up-stream for retieving subseq using BED (--beb) or GTF (--gtf) file.

• seqkit locate: add flag -G/--non-greedy, non-greedy mode,
  faster but may miss motifs overlaping with others. Example:

  • greedy mode (default)

       $ echo -e '>seq\nACGACGACGA' | seqkit locate -p ACGA | csvtk -t pretty
       seqID   patternName   pattern   strand   start   end   matched
       seq     ACGA          ACGA      +        1       4     ACGA
       seq     ACGA          ACGA      +        4       7     ACGA
       seq     ACGA          ACGA      +        7       10    ACGA
    

  • non-greedy mode (-G)

      $ echo -e '>seq\nACGACGACGA' | seqkit locate -p ACGA -G | csvtk -t pretty
      seqID   patternName   pattern   strand   start   end   matched
      seq     ACGA          ACGA      +        1       4     ACGA
      seq     ACGA          ACGA      +        7       10    ACGA
    

SeqKit v0.5.1

Changelog

• seqkit restart: fix bug of flag parsing

SeqKit v0.5.0

Changelog

• new command seqkit restart, for resetting start position for circular genome.
• seqkit sliding: add flag -g/--greedy, exporting last subsequences even shorter than windows size.
• seqkit seq:
  • add flag -m/--min-len and -M/--max-len to filter sequences by length.
  • rename flag -G/--gap-letter to -G/--gap-letters.
• seqkit stat:
  • renamed to seqkit stats, don't worry, old name is still available as an alias.
  • add new flag -a/all, for all statistics, including sum_gap, N50, and L50.

SeqKit v0.4.5

Changelog

• seqkit seq: fix bug of failing to reverse quality of FASTQ sequence

SeqKit v0.4.4

Changelog

• seqkit locate: fix bug of missing regular-expression motifs containing
  non-DNA characters (e.g., ACT.{6,7}CGG) from motif file (-f).
• compiled with go v1.8.

SeqKit v0.4.3

Changelog

• fix bug of seqkit stat: min_len always be 0 in versions: v0.4.0, v0.4.1, v0.4.2

SeqKit v0.4.2

Changelog

• fix header information of seqkit subseq when restriving up- and down-steam
  sequences using GTF/BED file.

SeqKit v0.4.1

_64-bit versions are highly recommended._

Changelog

• enchancement: remove redudant regions for seqkit locate. e.g.:

  previous version:

  $ echo -ne ">test\nAACGcgcA" | seqkit locate -i -P -p "(CG)+"
  seqID   patternName     pattern strand  start   end     matched
  test    (CG)+   (CG)+   +       3       6       CGcg
  test    (CG)+   (CG)+   +       5       6       cg
  

  current version:

  $ echo -ne ">test\nAACGcgcA" | ./seqkit locate -i -P -p "(CG)+"
  seqID   patternName     pattern strand  start   end     matched
  test    (CG)+   (CG)+   +       3       6       CGcg