fakit v0.2.4.1

• fix several bugs from library bio, affected situations:
  • Locating patterns in sequences by pattern FASTA file: fakit locate -f
  • Reading FASTQ file with record of which the quality starts with +
• add command version which could check for update

_Recompiled at 2016-06-06 due to changed output of subcommand version_

fakit v0.2.4

• add subcommand head

_Recompiled at 2016-05-29 14:03:04 UTC, due to dependency bugs_

fakit v0.2.3

• reduce memory occupation by avoid copy data when convert string to []byte
• speedup reverse-complement by avoid repeatedly calling functions

fakit v0.2.2 optimization never stop

• reduce memory occupation of subcommands that use FASTA index

fakit v0.2.1 with further performance improvement of outputing

• _with further performance improvement of outputing_
• fix bug of fakit seq -g for FASTA fromat
• some other minor fix of code and docs
• update benchmark results

fakit v0.2.0 with lower memory usage

• _reduce memory usage of writing output_
• fix bug of subseq, shuffle, sort when reading from stdin
• reduce memory usage of faidx
• make validating sequences an optional option in seq command, it saves some time.

fakit v0.1.9

• using custom FASTA index file extension: .fakit.fai
• reducing memory usage of sample --number --two-pass
• _change default CPU number to 2 for multi-cpus computer, and 1 for single-CPU computer_
• and some optimizations
• update benchmark and docs.

fakit v0.1.8 utilizes faidx to improve performance and reduce memory usage

• add subcommand rename to rename duplicated IDs
• add subcommand faidx to create FASTA index file
• _utilize faidx to improve performance of subseq_
• _shuffle, sort and split support two-pass mode (by flag -2) with faidx to reduce memory usage._
• document updates

fakit v0.1.7 with support for (multi-line) FASTQ format

• _add support for (multi-line) FASTQ format_
• update document, add technical details
• rename subcommands fa2tab and tab2fa to fx2tab and tab2fx
• add subcommand fq2fa
• add column "seq_format" to stat
• add global flag -b (--bufer-size)
• little change of flag in subseq and some other commands

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