[med-svn] [Git][med-team/seqkit][master] 6 commits: routine-update: New upstream version
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun Sep 26 19:26:52 BST 2021
Nilesh Patra pushed to branch master at Debian Med / seqkit
Commits:
6e9257b1 by Nilesh Patra at 2021-09-26T23:37:33+05:30
routine-update: New upstream version
- - - - -
eb1d2ff1 by Nilesh Patra at 2021-09-26T23:37:35+05:30
New upstream version 2.0.1+ds
- - - - -
889a4c33 by Nilesh Patra at 2021-09-26T23:38:07+05:30
Update upstream source from tag 'upstream/2.0.1+ds'
Update to upstream version '2.0.1+ds'
with Debian dir 969c733e28248154d6861c503ae3f89a3566e74f
- - - - -
5d717c1f by Nilesh Patra at 2021-09-26T23:38:08+05:30
routine-update: Standards-Version: 4.6.0
- - - - -
fa90c321 by Nilesh Patra at 2021-09-26T23:48:27+05:30
Refresh patches
- - - - -
83f9d7b5 by Nilesh Patra at 2021-09-26T23:52:08+05:30
Upload to unstable
- - - - -
12 changed files:
- debian/changelog
- debian/control
- debian/patches/spellings.patch
- debian/patches/use-upstream-go-logger.patch
- doc/docs/download.md
- doc/docs/usage.md
- go.mod
- go.sum
- seqkit/cmd/grep.go
- seqkit/cmd/replace.go
- seqkit/cmd/subseq.go
- seqkit/main.go
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+seqkit (2.0.1+ds-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.0 (routine-update)
+ * Refresh patches
+
+ -- Nilesh Patra <nilesh at debian.org> Sun, 26 Sep 2021 23:48:31 +0530
+
seqkit (2.0.0+ds-1) unstable; urgency=medium
* New upstream version 2.0.0+ds
=====================================
debian/control
=====================================
@@ -27,7 +27,7 @@ Build-Depends: debhelper-compat (= 13),
golang-github-smallfish-simpleyaml-dev,
golang-github-twotwotwo-sorts-dev,
samtools
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/seqkit
Vcs-Git: https://salsa.debian.org/med-team/seqkit.git
Homepage: https://github.com/shenwei356/seqkit
=====================================
debian/patches/spellings.patch
=====================================
@@ -44,7 +44,7 @@ Last Changed: August 3, 2020
--- a/seqkit/cmd/replace.go
+++ b/seqkit/cmd/replace.go
-@@ -234,7 +234,7 @@
+@@ -241,7 +241,7 @@
"ATTENTION: for *nix OS, use SINGLE quote NOT double quotes or "+
`use the \ escape character. Record number is also supported by "{nr}".`+
`use ${1} instead of $1 when {kv} given!`)
=====================================
debian/patches/use-upstream-go-logger.patch
=====================================
@@ -9,7 +9,7 @@ Last changed: Mon June 29 2020
colorable "github.com/mattn/go-colorable"
- "github.com/shenwei356/go-logging"
+ "github.com/op/go-logging"
- "github.com/shenwei356/seqkit/seqkit/cmd"
+ "github.com/shenwei356/seqkit/v2/seqkit/cmd"
)
--- a/seqkit/cmd/logging.go
=====================================
doc/docs/download.md
=====================================
@@ -3,21 +3,19 @@
SeqKit is implemented in [Go](https://golang.org/) programming language,
statically-linked executable binary files are [freely available](https://github.com/shenwei356/seqkit/releases).
-Please cite:
-
-> **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
-> ***PLOS ONE***. [doi:10.1371/journal.pone.0163962](https://doi.org/10.1371/journal.pone.0163962).
+Please cite: **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
+***PLOS ONE***. [doi:10.1371/journal.pone.0163962](https://doi.org/10.1371/journal.pone.0163962).
OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_linux_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_linux_386.tar.gz)
-Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_linux_amd64.tar.gz)
-Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_linux_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_linux_arm64.tar.gz)
-macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_darwin_amd64.tar.gz)
-macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_darwin_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_darwin_arm64.tar.gz)
-Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_windows_386.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz)|[](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/seqkit_windows_amd64.exe.tar.gz)
+Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_linux_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_linux_386.tar.gz)
+Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_linux_amd64.tar.gz)
+Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_linux_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_linux_arm64.tar.gz)
+macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_darwin_amd64.tar.gz)
+macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_darwin_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_windows_386.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz)|[](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/seqkit_windows_amd64.exe.tar.gz)
*Notes*
@@ -49,13 +47,13 @@ And then:
conda install -c bioconda seqkit
-#### Method 3: Install via homebrew (latest stable version)
+#### Method 3: Install via [homebrew](https://brew.sh/) (latest stable version)
- brew install brewsci/bio/seqkit
+ brew install seqkit
#### Method 4: For Go developer (latest stable/dev version)
- go get -u github.com/shenwei356/seqkit/seqkit
+ go get -u github.com/shenwei356/seqkit/v2/seqkit/
#### Method 5: Docker based installation (latest stable/dev version)
=====================================
doc/docs/usage.md
=====================================
@@ -425,7 +425,13 @@ Usage
``` text
get subsequences by region/gtf/bed, including flanking sequences.
-Recommendation: use plain FASTA file, so seqkit could utilize FASTA index.
+Attentions:
+ 1. Use "seqkit grep" for extract subsets of sequences.
+ "seqtk subseq seqs.fasta id.txt" equals to
+ "seqkit grep -f id.txt seqs.fasta"
+
+Recommendation:
+ 1. use plain FASTA file, so seqkit could utilize FASTA index.
The definition of region is 1-based and with some custom design.
@@ -1407,6 +1413,8 @@ Attentions:
file, not the order of the query patterns.
But for FASTA file, you can use:
seqkit faidx seqs.fasta --infile-list IDs.txt
+ 6. For multiple patterns, you can either set "-p" multiple times, i.e.,
+ -p pattern1 -p pattern2, or give a file of patterns via "-f/--pattern-file".
You can specify the sequence region for searching with the flag -R (--region).
The definition of region is 1-based and with some custom design.
@@ -2539,6 +2547,13 @@ Special replacement symbols (only for replacing name not sequence):
{nr} Record number, starting from 1
{kv} Corresponding value of the key (captured variable $n) by key-value file,
n can be specified by flag -I (--key-capt-idx) (default: 1)
+
+Special cases:
+ 1. If replacements contain '$',
+ a). If using '{kv}', you need use '$$$$' instead of a single '$':
+ -r '{kv}' -k <(sed 's/\$/$$$$/' kv.txt)
+ b). If not, use '$$':
+ -r 'xxx$$xx'
Usage:
seqkit replace [flags]
=====================================
go.mod
=====================================
@@ -1,4 +1,4 @@
-module github.com/shenwei356/seqkit
+module github.com/shenwei356/seqkit/v2
go 1.17
@@ -17,12 +17,11 @@ require (
github.com/mattn/go-isatty v0.0.13
github.com/mitchellh/go-homedir v1.1.0
github.com/pkg/errors v0.9.1
- github.com/pkg/profile v1.6.0
- github.com/shenwei356/bio v0.3.0
- github.com/shenwei356/breader v0.3.0
+ github.com/shenwei356/bio v0.3.1
+ github.com/shenwei356/breader v0.3.1
github.com/shenwei356/bwt v0.5.1
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
- github.com/shenwei356/util v0.3.0
+ github.com/shenwei356/util v0.3.2
github.com/shenwei356/xopen v0.1.0
github.com/smallfish/simpleyaml v0.1.0
github.com/spf13/cobra v1.2.1
@@ -37,7 +36,7 @@ require (
github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 // indirect
github.com/inconshreveable/mousetrap v1.0.0 // indirect
github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5 // indirect
- github.com/klauspost/compress v1.13.4 // indirect
+ github.com/klauspost/compress v1.13.6 // indirect
github.com/mattn/go-runewidth v0.0.13 // indirect
github.com/rivo/uniseg v0.2.0 // indirect
github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 // indirect
=====================================
go.sum
=====================================
@@ -132,7 +132,6 @@ github.com/golang/protobuf v1.4.3/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw
github.com/golang/protobuf v1.5.0/go.mod h1:FsONVRAS9T7sI+LIUmWTfcYkHO4aIWwzhcaSAoJOfIk=
github.com/golang/protobuf v1.5.1/go.mod h1:DopwsBzvsk0Fs44TXzsVbJyPhcCPeIwnvohx4u74HPM=
github.com/golang/protobuf v1.5.2/go.mod h1:XVQd3VNwM+JqD3oG2Ue2ip4fOMUkwXdXDdiuN0vRsmY=
-github.com/golang/snappy v0.0.3/go.mod h1:/XxbfmMg8lxefKM7IXC3fBNl/7bRcc72aCRzEWrmP2Q=
github.com/google/btree v0.0.0-20180813153112-4030bb1f1f0c/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=
github.com/google/btree v1.0.0/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=
github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M=
@@ -201,8 +200,8 @@ github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5 h1:PJr+ZMXIecYc
github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5/go.mod h1:7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes=
github.com/kisielk/errcheck v1.5.0/go.mod h1:pFxgyoBC7bSaBwPgfKdkLd5X25qrDl4LWUI2bnpBCr8=
github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck=
-github.com/klauspost/compress v1.13.4 h1:0zhec2I8zGnjWcKyLl6i3gPqKANCCn5e9xmviEEeX6s=
-github.com/klauspost/compress v1.13.4/go.mod h1:8dP1Hq4DHOhN9w426knH3Rhby4rFm6D8eO+e+Dq5Gzg=
+github.com/klauspost/compress v1.13.6 h1:P76CopJELS0TiO2mebmnzgWaajssP/EszplttgQxcgc=
+github.com/klauspost/compress v1.13.6/go.mod h1:/3/Vjq9QcHkK5uEr5lBEmyoZ1iFhe47etQ6QUkpK6sk=
github.com/klauspost/pgzip v1.2.5 h1:qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE=
github.com/klauspost/pgzip v1.2.5/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=
github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560/go.mod h1:oDr41C7kH9wvAikWyFhr6UFr8R7nelpmCF5XR5rL7I8=
@@ -245,8 +244,6 @@ github.com/pelletier/go-toml v1.9.3/go.mod h1:u1nR/EPcESfeI/szUZKdtJ0xRNbUoANCko
github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4=
github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
-github.com/pkg/profile v1.6.0 h1:hUDfIISABYI59DyeB3OTay/HxSRwTQ8rB/H83k6r5dM=
-github.com/pkg/profile v1.6.0/go.mod h1:qBsxPvzyUincmltOk6iyRVxHYg4adc0OFOv72ZdLa18=
github.com/pkg/sftp v1.10.1/go.mod h1:lYOWFsE0bwd1+KfKJaKeuokY15vzFx25BLbzYYoAxZI=
github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
@@ -261,20 +258,20 @@ github.com/rogpeppe/go-internal v1.3.0/go.mod h1:M8bDsm7K2OlrFYOpmOWEs/qY81heoFR
github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
github.com/ryanuber/columnize v0.0.0-20160712163229-9b3edd62028f/go.mod h1:sm1tb6uqfes/u+d4ooFouqFdy9/2g9QGwK3SQygK0Ts=
github.com/sean-/seed v0.0.0-20170313163322-e2103e2c3529/go.mod h1:DxrIzT+xaE7yg65j358z/aeFdxmN0P9QXhEzd20vsDc=
-github.com/shenwei356/bio v0.3.0 h1:+QKBS2ehlQGeCmYZmr6xP8UiPdhRQI0uVH6KbYmXuIQ=
-github.com/shenwei356/bio v0.3.0/go.mod h1:dl64Vmd+iK1GOMZwT7XpliFN9yTmeE9+pW7SEHEXDQQ=
+github.com/shenwei356/bio v0.3.1 h1:rdSoslv8HahfJpkzhN6W1Ky1lQ++gaBIfuJAC4f65cc=
+github.com/shenwei356/bio v0.3.1/go.mod h1:rHA8DoaDooXKdqX7bqoksQDKm3mEAQ3MsD9nivVTSf0=
github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 h1:/3JklLnHXiWUBxWc3joQYavDQJpncRhRA909cUb7eOw=
github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403/go.mod h1:YkgdTWfNnJgv5HVJbVSDmxQtkK3/jZWDoqcG26BVU8k=
-github.com/shenwei356/breader v0.3.0 h1:RwAhiE8xkS4OLawSbtzP6w0KGrh6W1zmRachfzkOVPE=
-github.com/shenwei356/breader v0.3.0/go.mod h1:dyV4ivjTV0hwP627/FQAYFgpMYEeKQYHlKs3E5iY4Dw=
+github.com/shenwei356/breader v0.3.1 h1:OjgfeHhpNGQPkS1+lgsl4eNuuO//Y16N6TkqG5oxO5U=
+github.com/shenwei356/breader v0.3.1/go.mod h1:UR11JJCxU9s7eUdU4xn3L/VodxoXzWhjJPh8WZbb+us=
github.com/shenwei356/bwt v0.5.1 h1:pq9KxkJPwzUwPjwWqfTOkUmzwHm8JtMkZxBkqkzuIVo=
github.com/shenwei356/bwt v0.5.1/go.mod h1:V2hX4adhr4WfFpy2ogKiV8A2WO9FeK0wkq1o3/R91mE=
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba h1:UvnrxFDPmz7agYX0eQ2JEorTKn1ORnZ9dT5OzbjPvK8=
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba/go.mod h1:LiqYp/K5yCEWOi7Ux/iOF/kjDxtsdYjOGcKHDbEOXFU=
github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d h1:eeXLHcXyGEr72V1SOSEI7vSzUOTJvHutwF7Ykm+hscQ=
github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d/go.mod h1:SiiGiRFyRtV7S9RamOrmQR5gpGIRhWJM1w0EtmuQ1io=
-github.com/shenwei356/util v0.3.0 h1:gTVa3sGwcyGEHgNpXTzdL3MaaJN/bGAypVKSCnT4QfU=
-github.com/shenwei356/util v0.3.0/go.mod h1:n3qhc3bQzlqJ2/5v79hgl0Gd3WzJOkI8XcUix25Brdg=
+github.com/shenwei356/util v0.3.2 h1:3qXkcO2erNKnPCnV8zxjN2JL5sGnOqW+muj1x4XxkuM=
+github.com/shenwei356/util v0.3.2/go.mod h1:pY/f5wR/0o0dJcodhw1Df/ghzqNt2wFSATW0zymI4mA=
github.com/shenwei356/xopen v0.1.0 h1:PizY52rLA7A6EdkwKZ6A8h8/a+c9DCBXqfLtwVzsWnM=
github.com/shenwei356/xopen v0.1.0/go.mod h1:6EQUa6I7Zsl2GQKqcL9qGLrTzVE+oZyly+uhzovQYSk=
github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc=
=====================================
seqkit/cmd/grep.go
=====================================
@@ -70,6 +70,8 @@ Attentions:
file, not the order of the query patterns.
But for FASTA file, you can use:
seqkit faidx seqs.fasta --infile-list IDs.txt
+ 6. For multiple patterns, you can either set "-p" multiple times, i.e.,
+ -p pattern1 -p pattern2, or give a file of patterns via "-f/--pattern-file".
You can specify the sequence region for searching with the flag -R (--region).
The definition of region is 1-based and with some custom design.
=====================================
seqkit/cmd/replace.go
=====================================
@@ -58,6 +58,13 @@ Special replacement symbols (only for replacing name not sequence):
{nr} Record number, starting from 1
{kv} Corresponding value of the key (captured variable $n) by key-value file,
n can be specified by flag -I (--key-capt-idx) (default: 1)
+
+Special cases:
+ 1. If replacements contain '$',
+ a). If using '{kv}', you need use '$$$$' instead of a single '$':
+ -r '{kv}' -k <(sed 's/\$/$$$$/' kv.txt)
+ b). If not, use '$$':
+ -r 'xxx$$xx'
`,
Run: func(cmd *cobra.Command, args []string) {
@@ -144,7 +151,7 @@ Special replacement symbols (only for replacing name not sequence):
var r []byte
var founds [][][]byte
var found [][]byte
- var k string
+ var k, v string
var ok bool
var doNotChange bool
var record *fastx.Record
@@ -198,8 +205,8 @@ Special replacement symbols (only for replacing name not sequence):
if ignoreCase {
k = strings.ToLower(k)
}
- if _, ok = kvs[k]; ok {
- r = reKV.ReplaceAll(r, []byte(kvs[k]))
+ if v, ok = kvs[k]; ok {
+ r = reKV.ReplaceAll(r, []byte(v))
} else if keepUntouch {
doNotChange = true
} else if keepKey {
=====================================
seqkit/cmd/subseq.go
=====================================
@@ -43,7 +43,13 @@ var subseqCmd = &cobra.Command{
Short: "get subsequences by region/gtf/bed, including flanking sequences",
Long: fmt.Sprintf(`get subsequences by region/gtf/bed, including flanking sequences.
-Recommendation: use plain FASTA file, so seqkit could utilize FASTA index.
+Attentions:
+ 1. Use "seqkit grep" for extract subsets of sequences.
+ "seqtk subseq seqs.fasta id.txt" equals to
+ "seqkit grep -f id.txt seqs.fasta"
+
+Recommendation:
+ 1. use plain FASTA file, so seqkit could utilize FASTA index.
The definition of region is 1-based and with some custom design.
=====================================
seqkit/main.go
=====================================
@@ -27,7 +27,7 @@ import (
colorable "github.com/mattn/go-colorable"
"github.com/shenwei356/go-logging"
- "github.com/shenwei356/seqkit/seqkit/cmd"
+ "github.com/shenwei356/seqkit/v2/seqkit/cmd"
)
var logFormat = logging.MustStringFormatter(
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/f2a1a629c260a9870756823a3965f1a832691de3...83f9d7b53389e1238aae90a45f61b086f8256bb9
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/f2a1a629c260a9870756823a3965f1a832691de3...83f9d7b53389e1238aae90a45f61b086f8256bb9
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