[med-svn] [Git][med-team/seqkit][upstream] New upstream version 2.1.0+ds
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun Jan 16 13:34:27 GMT 2022
Nilesh Patra pushed to branch upstream at Debian Med / seqkit
Commits:
5388a29b by Nilesh Patra at 2022-01-16T18:15:51+05:30
New upstream version 2.1.0+ds
- - - - -
23 changed files:
- − .travis.yml
- CHANGELOG.md
- README.md
- doc/docs/download.md
- go.mod
- go.sum
- seqkit/cmd/amplicon.go
- seqkit/cmd/bam.go
- seqkit/cmd/bed.go
- seqkit/cmd/faidx.go
- seqkit/cmd/fq2fa.go
- seqkit/cmd/fx2tab.go
- seqkit/cmd/grep.go
- seqkit/cmd/locate.go
- seqkit/cmd/mutate.go
- seqkit/cmd/pair.go
- seqkit/cmd/replace.go
- seqkit/cmd/root.go
- seqkit/cmd/scat.go
- seqkit/cmd/shuffle.go
- seqkit/cmd/sort.go
- seqkit/cmd/split.go
- tests/test.sh
Changes:
=====================================
.travis.yml deleted
=====================================
@@ -1,28 +0,0 @@
-language: go
-
-jobs:
- include:
- - os: linux
- dist: bionic
- - os: osx
- osx_image: xcode10
-
-go:
- - 1.x
-
-cache: miniconda3
-
-before_install:
- - if [ $TRAVIS_OS_NAME = "linux" ]; then wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi;
- - if [ $TRAVIS_OS_NAME = "osx" ]; then wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi;
- - bash ./miniconda.sh -u -b -p ./miniconda3 && source ./miniconda3/bin/activate;
- - conda init bash && source $HOME/.bashrc;
- - conda update -q --yes conda;
- - conda update -q --yes --all;
- - conda config --add channels conda-forge;
- - conda config --add channels conda-forge;
- - conda install -q --yes sed openssl;
-
-
-script:
- - ./tests/test.sh
=====================================
CHANGELOG.md
=====================================
@@ -1,3 +1,18 @@
+- [SeqKit v2.1.0](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0) - 2021-11-15
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0)
+ - `seqkit seq`:
+ - **fix filtering by average quality `-Q/-R`**. [#257](https://github.com/shenwei356/seqkit/issues/257)
+ - `seqkit convert`:
+ - fix quality encoding checking, change default value of `-N/--thresh-B-in-n-most-common` from `4` to `2`.
+ [#254](https://github.com/shenwei356/seqkit/issues/254) and [#239](https://github.com/shenwei356/seqkit/issues/239])
+ - `seqkit split`:
+ - fix writing an extra empty file when using `--two-pass`[#244](https://github.com/shenwei356/seqkit/issues/244)
+ - `seqkit subseq`:
+ - fix `--bed` which fail to recognize strand `.`.
+ - `seqkit fq2fa`:
+ - faster, and do not wrap sequences.
+ - `seqkit grep/locate/mutate`:
+ - detect unquoted comma and show warning message, e.g., `-p 'A{2,}'`. [#250](https://github.com/shenwei356/seqkit/issues/250)
- [SeqKit v2.0.0](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0) - 2021-08-27
[](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0)
- **Performance improvements**
=====================================
README.md
=====================================
@@ -67,7 +67,7 @@ install via conda:
| |[common](https://bioinf.shenwei.me/seqkit/usage/#common) |find common sequences of multiple files by id/name/sequence |FASTA/Q |+ and - | | |
| |[duplicate](https://bioinf.shenwei.me/seqkit/usage/#duplicate) |duplicate sequences N times |FASTA/Q | | |★ |
| |[split](https://bioinf.shenwei.me/seqkit/usage/#split) |split sequences into files by id/seq region/size/parts (mainly for FASTA) |FASTA preffered| | |★ |
-| |[spit2](https://bioinf.shenwei.me/seqkit/usage/#spit2) |split sequences into files by size/parts (FASTA, PE/SE FASTQ) |FASTA/Q | | |★★ |
+| |[split2](https://bioinf.shenwei.me/seqkit/usage/#split2) |split sequences into files by size/parts (FASTA, PE/SE FASTQ) |FASTA/Q | | |★★ |
| |[head](https://bioinf.shenwei.me/seqkit/usage/#head) |print first N FASTA/Q records |FASTA/Q | | | |
| |[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome) |print sequences of the first genome with common prefixes in name |FASTA/Q | | | |
| |[range](https://bioinf.shenwei.me/seqkit/usage/#range) |print FASTA/Q records in a range (start:end) |FASTA/Q | | | |
=====================================
doc/docs/download.md
=====================================
@@ -9,13 +9,13 @@ Please cite: **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultr
OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-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)
+Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_linux_386.tar.gz)
+Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_linux_amd64.tar.gz)
+Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_linux_arm64.tar.gz)
+macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_darwin_amd64.tar.gz)
+macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_windows_amd64.exe.tar.gz)
*Notes*
@@ -98,6 +98,21 @@ fish:
## Release History
+- [SeqKit v2.1.0](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0) - 2021-11-15
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0)
+ - `seqkit seq`:
+ - **fix filtering by average quality `-Q/-R`**. [#257](https://github.com/shenwei356/seqkit/issues/257)
+ - `seqkit convert`:
+ - fix quality encoding checking, change default value of `-N/--thresh-B-in-n-most-common` from `4` to `2`.
+ [#254](https://github.com/shenwei356/seqkit/issues/254) and [#239](https://github.com/shenwei356/seqkit/issues/239])
+ - `seqkit split`:
+ - fix writing an extra empty file when using `--two-pass`[#244](https://github.com/shenwei356/seqkit/issues/244)
+ - `seqkit subseq`:
+ - fix `--bed` which fail to recognize strand `.`.
+ - `seqkit fq2fa`:
+ - faster, and do not wrap sequences.
+ - `seqkit grep/locate/mutate`:
+ - detect unquoted comma and show warning message, e.g., `-p 'A{2,}'`. [#250](https://github.com/shenwei356/seqkit/issues/250)
- [SeqKit v2.0.0](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0) - 2021-08-27
[](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0)
- **Performance improvements**
=====================================
go.mod
=====================================
@@ -13,15 +13,15 @@ require (
github.com/iafan/cwalk v0.0.0-20210125030640-586a8832a711
github.com/klauspost/pgzip v1.2.5
github.com/logrusorgru/aurora v2.0.3+incompatible
- github.com/mattn/go-colorable v0.1.8
- github.com/mattn/go-isatty v0.0.13
+ github.com/mattn/go-colorable v0.1.11
+ github.com/mattn/go-isatty v0.0.14
github.com/mitchellh/go-homedir v1.1.0
github.com/pkg/errors v0.9.1
- github.com/shenwei356/bio v0.3.1
+ github.com/shenwei356/bio v0.6.0
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 v0.3.2
+ github.com/shenwei356/util v0.5.0
github.com/shenwei356/xopen v0.1.0
github.com/smallfish/simpleyaml v0.1.0
github.com/spf13/cobra v1.2.1
@@ -39,12 +39,11 @@ require (
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
github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d // indirect
github.com/spf13/pflag v1.0.5 // indirect
golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9 // indirect
golang.org/x/image v0.0.0-20190802002840-cff245a6509b // indirect
- golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c // indirect
+ golang.org/x/sys v0.0.0-20210927094055-39ccf1dd6fa6 // indirect
gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b // indirect
gopkg.in/yaml.v2 v2.4.0 // indirect
)
=====================================
go.sum
=====================================
@@ -217,12 +217,11 @@ github.com/logrusorgru/aurora v2.0.3+incompatible h1:tOpm7WcpBTn4fjmVfgpQq0EfczG
github.com/logrusorgru/aurora v2.0.3+incompatible/go.mod h1:7rIyQOR62GCctdiQpZ/zOJlFyk6y+94wXzv6RNZgaR4=
github.com/magiconair/properties v1.8.5/go.mod h1:y3VJvCyxH9uVvJTWEGAELF3aiYNyPKd5NZ3oSwXrF60=
github.com/mattn/go-colorable v0.0.9/go.mod h1:9vuHe8Xs5qXnSaW/c/ABM9alt+Vo+STaOChaDxuIBZU=
-github.com/mattn/go-colorable v0.1.8 h1:c1ghPdyEDarC70ftn0y+A/Ee++9zz8ljHG1b13eJ0s8=
-github.com/mattn/go-colorable v0.1.8/go.mod h1:u6P/XSegPjTcexA+o6vUJrdnUu04hMope9wVRipJSqc=
+github.com/mattn/go-colorable v0.1.11 h1:nQ+aFkoE2TMGc0b68U2OKSexC+eq46+XwZzWXHRmPYs=
+github.com/mattn/go-colorable v0.1.11/go.mod h1:u5H1YNBxpqRaxsYJYSkiCWKzEfiAb1Gb520KVy5xxl4=
github.com/mattn/go-isatty v0.0.3/go.mod h1:M+lRXTBqGeGNdLjl/ufCoiOlB5xdOkqRJdNxMWT7Zi4=
-github.com/mattn/go-isatty v0.0.12/go.mod h1:cbi8OIDigv2wuxKPP5vlRcQ1OAZbq2CE4Kysco4FUpU=
-github.com/mattn/go-isatty v0.0.13 h1:qdl+GuBjcsKKDco5BsxPJlId98mSWNKqYA+Co0SC1yA=
-github.com/mattn/go-isatty v0.0.13/go.mod h1:cbi8OIDigv2wuxKPP5vlRcQ1OAZbq2CE4Kysco4FUpU=
+github.com/mattn/go-isatty v0.0.14 h1:yVuAays6BHfxijgZPzw+3Zlu5yQgKGP2/hcQbHb7S9Y=
+github.com/mattn/go-isatty v0.0.14/go.mod h1:7GGIvUiUoEMVVmxf/4nioHXj79iQHKdU27kJ6hsGG94=
github.com/mattn/go-runewidth v0.0.13 h1:lTGmDsbAYt5DmK6OnoV7EuIF1wEIFAcxld6ypU4OSgU=
github.com/mattn/go-runewidth v0.0.13/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
github.com/miekg/dns v1.0.14/go.mod h1:W1PPwlIAgtquWBMBEV9nkV9Cazfe8ScdGz/Lj7v3Nrg=
@@ -239,6 +238,7 @@ github.com/mitchellh/mapstructure v1.4.1/go.mod h1:bFUtVrKA4DC2yAKiSyO/QUcy7e+RR
github.com/modern-go/concurrent v0.0.0-20180228061459-e0a39a4cb421/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
github.com/modern-go/reflect2 v0.0.0-20180701023420-4b7aa43c6742/go.mod h1:bx2lNnkwVCuqBIxFjflWJWanXIb3RllmbCylyMrvgv0=
github.com/modern-go/reflect2 v1.0.1/go.mod h1:bx2lNnkwVCuqBIxFjflWJWanXIb3RllmbCylyMrvgv0=
+github.com/montanaflynn/stats v0.6.6/go.mod h1:etXPPgVO6n31NxCd9KQUMvCM+ve0ruNzt6R8Bnaayow=
github.com/pascaldekloe/goe v0.0.0-20180627143212-57f6aae5913c/go.mod h1:lzWF7FIEvWOWxwDKqyGYQf6ZUaNfKdP144TG7ZOy1lc=
github.com/pelletier/go-toml v1.9.3/go.mod h1:u1nR/EPcESfeI/szUZKdtJ0xRNbUoANCkoOuaOx1Y+c=
github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
@@ -258,20 +258,19 @@ 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 v0.3.1 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/bio v0.6.0 h1:od1J1/tpXZ5p6DiPa5kCM+ijl1uesSmndhmZkirnglE=
+github.com/shenwei356/bio v0.6.0/go.mod h1:LL8JBeJnKQ4esixngQZiTkZgO1/by1qI0XhMrUl7T8M=
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/kmers v0.1.0/go.mod h1:23Ltr95n98LYy9OtJMFSzkmU/1nmdYwgzqB3walAQ6g=
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 v0.3.2 h1:3qXkcO2erNKnPCnV8zxjN2JL5sGnOqW+muj1x4XxkuM=
-github.com/shenwei356/util v0.3.2/go.mod h1:pY/f5wR/0o0dJcodhw1Df/ghzqNt2wFSATW0zymI4mA=
+github.com/shenwei356/util v0.5.0 h1:gbPuGYVggNLOSORuZLnpaB2DrIpyDFolHiZQkyja+XU=
+github.com/shenwei356/util v0.5.0/go.mod h1:goFN/u2HgvfbOsEgoHA2hUEet+9KjZpRavrVGz9cm30=
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=
@@ -302,11 +301,13 @@ github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553 h1:DRC1ubdb3ZmyyIe
github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553/go.mod h1:Rj7Csq/tZ/egz+Ltc2IVpsA5309AmSMEswjkTZmq2Xc=
github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8=
github.com/ulikunitz/xz v0.5.10/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
+github.com/will-rowe/nthash v0.4.0/go.mod h1:5ezweuK0J5j+/7lih/RkrSmnxI3hoaPpQiVWJ7rd960=
github.com/yuin/goldmark v1.1.25/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
github.com/yuin/goldmark v1.1.27/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
github.com/yuin/goldmark v1.1.32/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
github.com/yuin/goldmark v1.2.1/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
github.com/yuin/goldmark v1.3.5/go.mod h1:mwnBkeHKe2W/ZEtQ+71ViKU8L12m81fl3OWwC1Zlc8k=
+github.com/zeebo/wyhash v0.0.1/go.mod h1:Ti+OwfNtM5AZiYAL0kOPIfliqDP5c0VtOnnMAqzuuZk=
go.etcd.io/etcd/api/v3 v3.5.0/go.mod h1:cbVKeC6lCfl7j/8jBhAK6aIYO9XOjdptoxU/nLQcPvs=
go.etcd.io/etcd/client/pkg/v3 v3.5.0/go.mod h1:IJHfcCEKxYu1Os13ZdwCwIUTUVGYTSAM3YSwc9/Ac1g=
go.etcd.io/etcd/client/v2 v2.305.0/go.mod h1:h9puh54ZTgAKtEbut2oe9P4L/oqKCVB6xsXlzd7alYQ=
@@ -444,7 +445,6 @@ golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7w
golang.org/x/sys v0.0.0-20191204072324-ce4227a45e2e/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20191228213918-04cbcbbfeed8/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20200113162924-86b910548bc1/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
-golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20200122134326-e047566fdf82/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20200202164722-d101bd2416d5/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20200212091648-12a6c2dcc1e4/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
@@ -470,8 +470,9 @@ golang.org/x/sys v0.0.0-20210320140829-1e4c9ba3b0c4/go.mod h1:h1NjWce9XRLGQEsW7w
golang.org/x/sys v0.0.0-20210330210617-4fbd30eecc44/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20210403161142-5e06dd20ab57/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20210510120138-977fb7262007/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
-golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c h1:F1jZWGFhYfh0Ci55sIpILtKKK8p3i2/krTr0H1rg74I=
golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.0.0-20210927094055-39ccf1dd6fa6 h1:foEbQz/B0Oz6YIqu/69kfXPYeFQAuuMYFkjaqXzl5Wo=
+golang.org/x/sys v0.0.0-20210927094055-39ccf1dd6fa6/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
golang.org/x/text v0.0.0-20170915032832-14c0d48ead0c/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
=====================================
seqkit/cmd/amplicon.go
=====================================
@@ -52,7 +52,7 @@ var ampliconCmd = &cobra.Command{
Attentions:
1. Only one (the longest) matching location is returned for every primer pair.
- 2. Mismatch is allowed, but the mismatch location (5' or 3') is not controled.
+ 2. Mismatch is allowed, but the mismatch location (5' or 3') is not controlled.
You can increase the value of "-j/--threads" to accelerate processing.
3. Degenerate bases/residues like "RYMM.." are also supported.
But do not use degenerate bases/residues in regular expression, you need
=====================================
seqkit/cmd/bam.go
=====================================
@@ -707,14 +707,14 @@ var bamCmd = &cobra.Command{
}
fmap["RefAln"] = fieldInfo{
- "Aligned refence length",
+ "Aligned reference length",
func(r *sam.Record) float64 {
return float64(r.Len())
},
}
fmap["RefCov"] = fieldInfo{
- "Refence coverage",
+ "Reference coverage",
func(r *sam.Record) float64 {
return float64(r.Len()) / float64(r.Ref.Len()) * 100
},
=====================================
seqkit/cmd/bed.go
=====================================
@@ -94,7 +94,7 @@ func ReadBedFilteredFeatures(file string, chrs []string) ([]BedFeature, error) {
}
var strand *string
if n >= 6 {
- if items[5] != "+" && items[5] != "-" {
+ if items[5] != "+" && items[5] != "-" && items[5] != "." {
return nil, false, fmt.Errorf("bad strand: %s", items[5])
}
strand = &items[5]
@@ -106,7 +106,7 @@ func ReadBedFilteredFeatures(file string, chrs []string) ([]BedFeature, error) {
if err != nil {
return nil, err
}
- BedFeatures := []BedFeature{}
+ BedFeatures := make([]BedFeature, 0, 1024)
for chunk := range reader.Ch {
if chunk.Err != nil {
return nil, chunk.Err
=====================================
seqkit/cmd/faidx.go
=====================================
@@ -264,7 +264,7 @@ type faidxQuery struct {
func init() {
RootCmd.AddCommand(faidxCmd)
- faidxCmd.Flags().BoolP("use-regexp", "r", false, "IDs are regular expression. But subseq region is not suppored here.")
+ faidxCmd.Flags().BoolP("use-regexp", "r", false, "IDs are regular expression. But subseq region is not supported here.")
faidxCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
faidxCmd.Flags().BoolP("full-head", "f", false, "print full header line instead of just ID. New fasta index file ending with .seqkit.fai will be created")
faidxCmd.Flags().StringP("region-file", "l", "", "file containing a list of regions")
=====================================
seqkit/cmd/fq2fa.go
=====================================
@@ -41,7 +41,7 @@ var fq2faCmd = &cobra.Command{
config := getConfigs(cmd)
alphabet := config.Alphabet
idRegexp := config.IDRegexp
- lineWidth := config.LineWidth
+ // lineWidth := config.LineWidth
outFile := config.OutFile
seq.AlphabetGuessSeqLengthThreshold = config.AlphabetGuessSeqLength
seq.ValidateSeq = false
@@ -70,7 +70,8 @@ var fq2faCmd = &cobra.Command{
}
record.Seq.Qual = []byte{}
- record.FormatToWriter(outfh, lineWidth)
+ // record.FormatToWriter(outfh, lineWidth)
+ record.FormatToWriter(outfh, 0)
}
}
},
=====================================
seqkit/cmd/fx2tab.go
=====================================
@@ -26,7 +26,6 @@ import (
"encoding/hex"
"fmt"
"io"
- "math"
"runtime"
"sort"
"strings"
@@ -212,7 +211,7 @@ Attention:
}
if printAvgQual {
- outfh.WriteString(fmt.Sprintf("\t%.2f", avgQual(record.Seq, qBase)))
+ outfh.WriteString(fmt.Sprintf("\t%.2f", record.Seq.AvgQual(qBase)))
}
if printSeqHash {
@@ -268,16 +267,4 @@ func alphabetStr(s []byte) string {
return strings.Join(alphabet, "")
}
-func avgQual(s *seq.Seq, base int) float64 {
- if len(s.Qual) == 0 {
- return 0
- }
- s.ParseQual(base)
- var sum float64
- for _, q := range s.QualValue {
- sum += math.Pow(10, float64(q)/-10)
- }
- return -10 * math.Log10(sum/float64(len(s.QualValue)))
-}
-
var _tab = []byte{'\t'}
=====================================
seqkit/cmd/grep.go
=====================================
@@ -114,6 +114,22 @@ Examples:
checkError(fmt.Errorf("one of flags -p (--pattern) and -f (--pattern-file) needed"))
}
+ // check pattern with unquoted comma
+ hasUnquotedComma := false
+ for _, _pattern := range pattern {
+ if reUnquotedComma.MatchString(_pattern) {
+ hasUnquotedComma = true
+ break
+ }
+ }
+ if hasUnquotedComma {
+ if outFile == "-" {
+ defer log.Warningf(helpUnquotedComma)
+ } else {
+ log.Warningf(helpUnquotedComma)
+ }
+ }
+
if degenerate && !bySeq {
log.Infof("when flag -d (--degenerate) given, flag -s (--by-seq) is automatically on")
bySeq = true
@@ -643,3 +659,6 @@ func init() {
grepCmd.Flags().BoolP("circular", "c", false, "circular genome")
grepCmd.Flags().BoolP("immediate-output", "I", false, "print output immediately, do not use write buffer")
}
+
+var reUnquotedComma = regexp.MustCompile(`\{[^\}]*$|^[^\{]*\}`)
+var helpUnquotedComma = `possible unquoted comma detected, please use double quotation marks for patterns containing comma, e.g., -p '"A{2,}"' or -p "\"A{2,}\""`
=====================================
seqkit/cmd/locate.go
=====================================
@@ -103,6 +103,22 @@ Attentions:
checkError(fmt.Errorf("one of flags -p (--pattern) and -f (--pattern-file) needed"))
}
+ // check pattern with unquoted comma
+ hasUnquotedComma := false
+ for _, _pattern := range pattern {
+ if reUnquotedComma.MatchString(_pattern) {
+ hasUnquotedComma = true
+ break
+ }
+ }
+ if hasUnquotedComma {
+ if outFile == "-" {
+ defer log.Warningf(helpUnquotedComma)
+ } else {
+ log.Warningf(helpUnquotedComma)
+ }
+ }
+
if mismatches > 0 {
if degenerate {
checkError(fmt.Errorf("flag -d (--degenerate) not allowed when giving flag -m (--max-mismatch)"))
@@ -906,6 +922,7 @@ Attentions:
}
}
}
+
},
}
=====================================
seqkit/cmd/mutate.go
=====================================
@@ -43,7 +43,7 @@ var mutateCmd = &cobra.Command{
Attentions:
- 1. Mutiple point mutations (-p/--point) are allowed, but only single
+ 1. Multiple point mutations (-p/--point) are allowed, but only single
insertion (-i/--insertion) OR single deletion (-d/--deletion) is allowed.
2. Point mutation takes place before insertion/deletion.
@@ -135,6 +135,22 @@ Examples:
// checkError(fmt.Errorf("one of flags -p (--pattern) and -f (--pattern-file) needed"))
// }
+ // check pattern with unquoted comma
+ hasUnquotedComma := false
+ for _, _pattern := range pattern {
+ if reUnquotedComma.MatchString(_pattern) {
+ hasUnquotedComma = true
+ break
+ }
+ }
+ if hasUnquotedComma {
+ if outFile == "-" {
+ defer log.Warningf(helpUnquotedComma)
+ } else {
+ log.Warningf(helpUnquotedComma)
+ }
+ }
+
// prepare pattern
patterns := make(map[string]*regexp.Regexp)
if patternFile != "" {
=====================================
seqkit/cmd/pair.go
=====================================
@@ -65,7 +65,7 @@ Attensions:
runtime.GOMAXPROCS(config.Threads)
if len(args) > 0 {
- checkError(errors.New("no positional arugments are allowed"))
+ checkError(errors.New("no positional arguments are allowed"))
}
read1 := getFlagString(cmd, "read1")
=====================================
seqkit/cmd/replace.go
=====================================
@@ -241,7 +241,7 @@ func init() {
"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!`)
- replaceCmd.Flags().IntP("nr-width", "", 1, `minimum width for {nr} in flag -r/--replacement. e.g., formating "1" to "001" by --nr-width 3`)
+ replaceCmd.Flags().IntP("nr-width", "", 1, `minimum width for {nr} in flag -r/--replacement. e.g., formatting "1" to "001" by --nr-width 3`)
// replaceCmd.Flags().BoolP("by-name", "n", false, "replace full name instead of just id")
replaceCmd.Flags().BoolP("by-seq", "s", false, "replace seq (only FASTA)")
replaceCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
=====================================
seqkit/cmd/root.go
=====================================
@@ -82,11 +82,14 @@ func init() {
}
RootCmd.PersistentFlags().StringP("seq-type", "t", "auto", "sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence)")
RootCmd.PersistentFlags().IntP("threads", "j", defaultThreads, "number of CPUs. can also set with environment variable SEQKIT_THREADS)")
- RootCmd.PersistentFlags().IntP("line-width", "w", 60, "line width when outputing FASTA format (0 for no wrap)")
+ RootCmd.PersistentFlags().IntP("line-width", "w", 60, "line width when outputting FASTA format (0 for no wrap)")
RootCmd.PersistentFlags().StringP("id-regexp", "", fastx.DefaultIDRegexp, "regular expression for parsing ID")
RootCmd.PersistentFlags().BoolP("id-ncbi", "", false, "FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud...")
RootCmd.PersistentFlags().StringP("out-file", "o", "-", `out file ("-" for stdout, suffix .gz for gzipped out)`)
RootCmd.PersistentFlags().BoolP("quiet", "", false, "be quiet and do not show extra information")
RootCmd.PersistentFlags().IntP("alphabet-guess-seq-length", "", 10000, "length of sequence prefix of the first FASTA record based on which seqkit guesses the sequence type (0 for whole seq)")
RootCmd.PersistentFlags().StringP("infile-list", "", "", "file of input files list (one file per line), if given, they are appended to files from cli arguments")
+
+ RootCmd.CompletionOptions.DisableDefaultCmd = true
+ RootCmd.SetHelpCommand(&cobra.Command{Hidden: true})
}
=====================================
seqkit/cmd/scat.go
=====================================
@@ -566,7 +566,7 @@ func init() {
scatCmd.Flags().StringP("in-format", "I", "", "input format: fastq or fasta (fastq)")
scatCmd.Flags().StringP("out-format", "O", "", "output format: fastq or fasta")
scatCmd.Flags().BoolP("allow-gaps", "A", false, "allow gap character (-) in sequences")
- scatCmd.Flags().BoolP("find-only", "f", false, "concatenate exisiting files and quit")
+ scatCmd.Flags().BoolP("find-only", "f", false, "concatenate existing files and quit")
scatCmd.Flags().BoolP("gz-only", "g", false, "only look for gzipped files (.gz suffix)")
scatCmd.Flags().StringP("time-limit", "T", "", "quit after inactive for this time period")
scatCmd.Flags().IntP("wait-pid", "p", -1, "after process with this PID exited")
=====================================
seqkit/cmd/shuffle.go
=====================================
@@ -46,7 +46,7 @@ For FASTA format, use flag -2 (--two-pass) to reduce memory usage. FASTQ not
supported.
Firstly, seqkit reads the sequence IDs. If the file is not plain FASTA file,
-seqkit will write the sequences to tempory files, and create FASTA index..
+seqkit will write the sequences to temporary files, and create FASTA index.
Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.
@@ -149,7 +149,7 @@ Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.
newFile = file + ".fastx"
}
if !quiet {
- log.Infof("read and write sequences to tempory file: %s ...", newFile)
+ log.Infof("read and write sequences to temporary file: %s ...", newFile)
}
var nseqs int
@@ -233,5 +233,5 @@ func init() {
RootCmd.AddCommand(shuffleCmd)
shuffleCmd.Flags().Int64P("rand-seed", "s", 23, "rand seed for shuffle")
shuffleCmd.Flags().BoolP("two-pass", "2", false, "two-pass mode read files twice to lower memory usage. (only for FASTA format)")
- shuffleCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")
+ shuffleCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")
}
=====================================
seqkit/cmd/sort.go
=====================================
@@ -50,7 +50,7 @@ supported.
Firstly, seqkit reads the sequence head and length information.
If the file is not plain FASTA file,
-seqkit will write the sequences to tempory files, and create FASTA index..
+seqkit will write the sequences to temporary files, and create FASTA index.
Secondly, seqkit sorts sequence by head and length information
and extracts sequences by FASTA index.
@@ -255,7 +255,7 @@ and extracts sequences by FASTA index.
newFile = file + ".fastx"
}
if !quiet {
- log.Infof("read and write sequences to tempory file: %s ...", newFile)
+ log.Infof("read and write sequences to temporary file: %s ...", newFile)
}
var nseqs int
@@ -463,6 +463,6 @@ func init() {
sortCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
sortCmd.Flags().BoolP("two-pass", "2", false, "two-pass mode read files twice to lower memory usage. (only for FASTA format)")
- sortCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")
+ sortCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")
sortCmd.Flags().IntP("seq-prefix-length", "L", 10000, "length of sequence prefix on which seqkit sorts by sequences (0 for whole sequence)")
}
=====================================
seqkit/cmd/split.go
=====================================
@@ -196,7 +196,7 @@ Examples:
newFile = file + ".fastx"
}
if !quiet {
- log.Infof("read and write sequences to tempory file: %s ...", newFile)
+ log.Infof("read and write sequences to temporary file: %s ...", newFile)
}
var nseqs int
@@ -362,7 +362,7 @@ Examples:
newFile = file + ".fastx"
}
if !quiet {
- log.Infof("read and write sequences to tempory file: %s ...", newFile)
+ log.Infof("read and write sequences to temporary file: %s ...", newFile)
}
var nseqs int
@@ -458,11 +458,17 @@ Examples:
j = 0
}
}
- if j > 0 && !quiet {
- log.Infof("write %d sequences to file: %s\n", j, outfile)
- }
- if !dryRun {
- outfh.Close()
+ if j > 0 {
+ if quiet {
+ log.Infof("write %d sequences to file: %s\n", j, outfile)
+ }
+ if !dryRun {
+ outfh.Close()
+ }
+ } else {
+ if !dryRun {
+ checkError(os.Remove(outfile))
+ }
}
if (isstdin || !isPlainFile(file)) && !keepTemp {
@@ -531,7 +537,7 @@ Examples:
newFile = file + ".fastx"
}
if !quiet {
- log.Infof("read and write sequences to tempory file: %s ...", newFile)
+ log.Infof("read and write sequences to temporary file: %s ...", newFile)
}
var nseqs int
@@ -555,7 +561,7 @@ Examples:
}
if isFastq {
checkError(os.Remove(newFile))
- checkError(fmt.Errorf("Sorry, two-pass mode does not support FASTQ format"))
+ checkError(fmt.Errorf("sorry, two-pass mode does not support FASTQ format"))
}
}
fileExt = suffixFA
@@ -722,7 +728,7 @@ Examples:
newFile = file + ".fastx"
}
if !quiet {
- log.Infof("read and write sequences to tempory file: %s ...", newFile)
+ log.Infof("read and write sequences to temporary file: %s ...", newFile)
}
var nseqs int
@@ -854,7 +860,7 @@ func init() {
`e.g 1:12 for first 12 bases, -12:-1 for last 12 bases. type "seqkit split -h" for more examples`)
splitCmd.Flags().BoolP("two-pass", "2", false, "two-pass mode read files twice to lower memory usage. (only for FASTA format)")
splitCmd.Flags().BoolP("dry-run", "d", false, "dry run, just print message and no files will be created.")
- splitCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")
+ splitCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")
splitCmd.Flags().StringP("out-dir", "O", "", "output directory (default value is $infile.split)")
splitCmd.Flags().BoolP("force", "f", false, "overwrite output directory")
}
=====================================
tests/test.sh
=====================================
@@ -203,7 +203,7 @@ assert_equal $(cat $STDOUT_FILE | md5sum | cut -d" " -f 1) $($app seq $file | md
file=tests/reads_1.fq.gz
run fq2fa $app fq2fa $file
-assert_equal $(cat $STDOUT_FILE | md5sum | cut -d" " -f 1) $($app fx2tab $file | cut -f 1,2 | $app tab2fx | md5sum | cut -d" " -f 1)
+assert_equal $(cat $STDOUT_FILE | md5sum | cut -d" " -f 1) $($app fx2tab $file | cut -f 1,2 | $app tab2fx -w 0 | md5sum | cut -d" " -f 1)
READS_FQ=tests/pcs109_5k.fq
NANO_FQ_TSV=tests/pcs109_5k_fq_NanoPlot.tsv
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/5388a29b97ce90095f23d015cbd4224431e555f4
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