Releases: shenwei356/seqkit
Releases · shenwei356/seqkit
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
andtab2fa
tofx2tab
andtab2fx
- 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
-
Remove descriptions
$ echo -e ">seq1 abc-123\nACGT-ACGT" | fakit replace -p " .+" >seq1 ACGT-ACGT
-
Replace "-" with "="
$ echo -e ">seq1 abc-123\nACGT-ACGT" | fakit replace -p "\-" -r '=' >seq1 abc=123 ACGT-ACGT
-
Remove gaps in sequences.
$ echo -e ">seq1 abc-123\nACGT-ACGT" | fakit replace -p " |-" -s >seq1 abc-123 ACGTACGT
-
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
-
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
fakit v0.1.5.2
- fix bug of
grep
, when not using flag-r
, flag-i
will not take effect.
fakit v0.1.5.1
- fix result of `fakit sample -n`
- fix benchmark scripts