[med-svn] [Git][med-team/seqkit][master] 3 commits: New upstream version 2.9.0+ds
Maytham Alsudany (@Maytha8)
gitlab at salsa.debian.org
Sat Feb 22 11:13:08 GMT 2025
Maytham Alsudany pushed to branch master at Debian Med / seqkit
Commits:
3d2db80b by Maytham Alsudany at 2025-01-09T19:57:56+08:00
New upstream version 2.9.0+ds
- - - - -
e8f5ea54 by Maytham Alsudany at 2025-01-09T19:57:56+08:00
Update upstream source from tag 'upstream/2.9.0+ds'
Update to upstream version '2.9.0+ds'
with Debian dir cab183427bfed25b28445ed10df81490056ecef2
- - - - -
41d03f49 by Maytham Alsudany at 2025-01-09T20:17:53+08:00
Upload to unstable
- - - - -
14 changed files:
- CHANGELOG.md
- README.md
- debian/changelog
- doc/docs/download.md
- doc/docs/usage.md
- go.mod
- go.sum
- seqkit/cmd/grep.go
- seqkit/cmd/helper.go
- seqkit/cmd/locate.go
- seqkit/cmd/replace.go
- seqkit/cmd/stat.go
- seqkit/cmd/version.go
- seqkit/packaging.sh
Changes:
=====================================
CHANGELOG.md
=====================================
@@ -1,3 +1,13 @@
+- [SeqKit v2.9.0](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0) - 2024-11-01
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0)
+ - `seqkit`:
+ - **Fix sequence ID parsing with the default regular expression (in this case, we actually use bytes.Index instead) for a rare case: "xxx\tyyy zzz" was wrongly parsed as "xxx\tyyy"**. [#486](https://github.com/shenwei356/seqkit/issues/486)
+ - `seqkit locate`:
+ - **Fix `-G/--non-greedy` for tandem repeats**, e.g., ATTCGATTCGATTCG (ATTCGx3).
+ - `seqkit grep/subseq`:
+ - Fix negative regions longer than sequence length. [#479](https://github.com/shenwei356/seqkit/issues/479).
+ - `seqkit stats`:
+ - Add an extra column `sum_n` to count the number of ambiguous characters. [#490](https://github.com/shenwei356/seqkit/issues/490)
- [SeqKit v2.8.2](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2) - 2024-05-17
[](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2)
- `seqkit amplicon`:
=====================================
README.md
=====================================
@@ -1,6 +1,6 @@
# SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
-
+- [**Try SeqKit in your browser**](https://sandbox.bio/tutorials/seqkit-intro) (Tutorials and Exercises provided by [sandbox.bio](https://sandbox.bio/tutorials/seqkit-intro))
- **Documents:** [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit)
([**Usage**](http://bioinf.shenwei.me/seqkit/usage/),
[**FAQs**](http://bioinf.shenwei.me/seqkit/faq/),
@@ -18,6 +18,7 @@ and
[](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=wHF3Lm8AAAAJ&citation_for_view=wHF3Lm8AAAAJ:zYLM7Y9cAGgC)
- **Others**: [](https://biotreasury.rjmart.cn/#/tool?id=10081)
+
<a href="https://doi.org/10.1002/imt2.191"><img src="seqkit2.jpg" alt="Subcommands of SeqKit2" width="700"/></a>
## Features
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+seqkit (2.9.0+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version 2.9.0
+
+ -- Maytham Alsudany <maytha8thedev at gmail.com> Thu, 09 Jan 2025 19:58:02 +0800
+
seqkit (2.8.2+ds-2) unstable; urgency=medium
* Fixup FTBFS with newer mpb (Closes: #1087554)
=====================================
doc/docs/download.md
=====================================
@@ -13,14 +13,17 @@ Please cite:
## Current Version
-- [SeqKit v2.8.2](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2) - 2024-05-17
-[](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2)
- - `seqkit amplicon`:
- - Fix a big introduced in v2.7.0. When more than one pairs of primers are given, only the last one is used. [#457](https://github.com/shenwei356/seqkit/issues/457)
- - `seqkit translate`:
- - Add option `-e/--skip-translate-errors` to skip translate error and output empty sequence. [#458](https://github.com/shenwei356/seqkit/pull/458)
- - `seqkit split`:
- - Add flag `-I/--ignore-case` for `-i/--by-id`. [#462](https://github.com/shenwei356/seqkit/issues/462)
+- [SeqKit v2.9.0](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0) - 2024-11-01
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0)
+ - `seqkit`:
+ - **Fix sequence ID parsing with the default regular expression (in this case, we actually use bytes.Index instead) for a rare case: "xxx\tyyy zzz" was wrongly parsed as "xxx\tyyy"**. [#486](https://github.com/shenwei356/seqkit/issues/486)
+ - `seqkit locate`:
+ - **Fix `-G/--non-greedy` for tandem repeats**, e.g., ATTCGATTCGATTCG (ATTCGx3).
+ - `seqkit grep/subseq`:
+ - Fix negative regions longer than sequence length. [#479](https://github.com/shenwei356/seqkit/issues/479).
+ - `seqkit stats`:
+ - Add an extra column `sum_n` to count the number of ambiguous characters. [#490](https://github.com/shenwei356/seqkit/issues/490)
+
@@ -29,13 +32,13 @@ Please cite:
OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_linux_386.tar.gz)
-Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_linux_amd64.tar.gz)
-Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_linux_arm64.tar.gz)
-macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_darwin_amd64.tar.gz)
-macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_darwin_arm64.tar.gz)
-Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_windows_amd64.exe.tar.gz)
+Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_linux_386.tar.gz)
+Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_linux_amd64.tar.gz)
+Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_linux_arm64.tar.gz)
+macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_darwin_amd64.tar.gz)
+macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_windows_amd64.exe.tar.gz)
*Notes*
@@ -157,6 +160,14 @@ fish:
## Release history
+- [SeqKit v2.8.2](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2) - 2024-05-17
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2)
+ - `seqkit amplicon`:
+ - Fix a big introduced in v2.7.0. When more than one pairs of primers are given, only the last one is used. [#457](https://github.com/shenwei356/seqkit/issues/457)
+ - `seqkit translate`:
+ - Add option `-e/--skip-translate-errors` to skip translate error and output empty sequence. [#458](https://github.com/shenwei356/seqkit/pull/458)
+ - `seqkit split`:
+ - Add flag `-I/--ignore-case` for `-i/--by-id`. [#462](https://github.com/shenwei356/seqkit/issues/462)
- [SeqKit v2.8.1](https://github.com/shenwei356/seqkit/releases/tag/v2.8.1) - 2024-04-07
[](https://github.com/shenwei356/seqkit/releases/tag/v2.8.1)
- `seqkit sana`:
=====================================
doc/docs/usage.md
=====================================
@@ -158,7 +158,7 @@ reproduced in different environments with same random seed.
``` text
SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
-Version: 2.8.0
+Version: 2.9.0
Author: Wei Shen <shenwei356 at gmail.com>
@@ -698,6 +698,7 @@ Columns:
16. Q30(%) percentage of bases with the quality score greater than 30
17. AvgQual average quality
18. GC(%) percentage of GC content
+ 19. sum_n number of ambitious letters (N, n, X, x)
Attention:
1. Sequence length metrics (sum_len, min_len, avg_len, max_len, Q1, Q2, Q3)
@@ -788,13 +789,13 @@ Eexamples
1. Extra information
$ seqkit stats *.f{a,q}.gz -a
- file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 N50_num Q20(%) Q30(%) AvgQual GC(%)
- hairpin.fa.gz FASTA RNA 28,645 2,949,871 39 103 2,354 76 91 111 0 101 380 0 0 0 45.77
- mature.fa.gz FASTA RNA 35,828 781,222 15 21.8 34 21 22 22 0 22 12 0 0 0 47.6
- Illimina1.8.fq.gz FASTQ DNA 10,000 1,500,000 150 150 150 150 150 150 0 150 1 96.16 89.71 24.82 49.91
- nanopore.fq.gz FASTQ DNA 4,000 1,798,723 153 449.7 6,006 271 318 391 0 395 585 40.79 12.63 9.48 46.66
- reads_1.fq.gz FASTQ DNA 2,500 567,516 226 227 229 227 227 227 0 227 3 91.24 86.62 15.45 53.63
- reads_2.fq.gz FASTQ DNA 2,500 560,002 223 224 225 224 224 224 0 224 2 91.06 87.66 14.62 54.77
+ file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 N50_num Q20(%) Q30(%) AvgQual GC(%) sum_n
+ hairpin.fa.gz FASTA RNA 28,645 2,949,871 39 103 2,354 76 91 111 0 101 380 0 0 0 45.77 255
+ mature.fa.gz FASTA RNA 35,828 781,222 15 21.8 34 21 22 22 0 22 12 0 0 0 47.6 0
+ Illimina1.8.fq.gz FASTQ DNA 10,000 1,500,000 150 150 150 150 150 150 0 150 1 96.16 89.71 24.82 49.91 38
+ nanopore.fq.gz FASTQ DNA 4,000 1,798,723 153 449.7 6,006 271 318 391 0 395 585 40.79 12.63 9.48 46.66 0
+ reads_1.fq.gz FASTQ DNA 2,500 567,516 226 227 229 227 227 227 0 227 3 91.24 86.62 15.45 53.63 44
+ reads_2.fq.gz FASTQ DNA 2,500 560,002 223 224 225 224 224 224 0 224 2 91.06 87.66 14.62 54.77 2
1. **Parallelize counting files, it's much faster for lots of small files, especially for files on SSD**
@@ -3091,7 +3092,9 @@ more on: http://bioinf.shenwei.me/seqkit/usage/#replace
Special replacement symbols (only for replacing name not sequence):
- {nr} Record number, starting from 1
+ {fn} File name
+ {fbn} File base name
+ {fbne} File base name without any extension
{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)
@@ -3236,6 +3239,13 @@ Examples
>seq_00002
ATTT
+1. Add file names.
+
+ $ seqkit replace ../tests/hairpin.fa -p '.+' -r '{fn}__{fbn}__{fbne}__{nr}' | seqkit seq -n | head -n 3
+ ../tests/hairpin.fa__hairpin.fa__hairpin__1
+ ../tests/hairpin.fa__hairpin.fa__hairpin__2
+ ../tests/hairpin.fa__hairpin.fa__hairpin__3
+
1. Replace key with value by key-value file
$ more test.fa
=====================================
go.mod
=====================================
@@ -20,12 +20,12 @@ require (
github.com/mattn/go-isatty v0.0.16
github.com/mitchellh/go-homedir v1.1.0
github.com/pkg/errors v0.9.1
- github.com/shenwei356/bio v0.13.3
+ github.com/shenwei356/bio v0.13.6
github.com/shenwei356/breader v0.3.2
github.com/shenwei356/bwt v0.6.1
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
github.com/shenwei356/stable v0.1.2
- github.com/shenwei356/util v0.5.2
+ github.com/shenwei356/util v0.5.3
github.com/shenwei356/xopen v0.3.2
github.com/smallfish/simpleyaml v0.1.0
github.com/spf13/cobra v1.8.0
=====================================
go.sum
=====================================
@@ -123,8 +123,8 @@ github.com/rogpeppe/go-internal v1.9.0/go.mod h1:WtVeX8xhTBvf0smdhujwtBcq4Qrzq/f
github.com/russross/blackfriday/v2 v2.1.0/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
github.com/ruudk/golang-pdf417 v0.0.0-20181029194003-1af4ab5afa58/go.mod h1:6lfFZQK844Gfx8o5WFuvpxWRwnSoipWe/p622j1v06w=
github.com/ruudk/golang-pdf417 v0.0.0-20201230142125-a7e3863a1245/go.mod h1:pQAZKsJ8yyVxGRWYNEm9oFB8ieLgKFnamEyDmSA0BRk=
-github.com/shenwei356/bio v0.13.3 h1:tWspivWisj/kS9RmDv8N0WEovn007jUImk8OdtPYZ38=
-github.com/shenwei356/bio v0.13.3/go.mod h1:5TMT6kpb5lQsa1Uz6nh6PGLtvKi8fQ3SWO2sfiBEOnc=
+github.com/shenwei356/bio v0.13.6 h1:GoJDNHNFIE6824IEAzBTf2f8BGqqshrIxgVxjlEHLRk=
+github.com/shenwei356/bio v0.13.6/go.mod h1:5TMT6kpb5lQsa1Uz6nh6PGLtvKi8fQ3SWO2sfiBEOnc=
github.com/shenwei356/breader v0.3.2 h1:GLy2clIMck6FdTwj8WLnmhv0PW/7Pp+Wcx7TVEHG0ks=
github.com/shenwei356/breader v0.3.2/go.mod h1:BimwolkMTIr/O4iX7xXtjEB1z5y39G+8I5Tsm9guC3E=
github.com/shenwei356/bwt v0.6.1 h1:BDS1nhhIxiC284OKtLBUgy+U5L/7WrvT/ehOExB/DSA=
@@ -135,8 +135,8 @@ github.com/shenwei356/natsort v0.0.0-20220117010048-580176ad49fb h1:pb0RhpaADsFr
github.com/shenwei356/natsort v0.0.0-20220117010048-580176ad49fb/go.mod h1:SiiGiRFyRtV7S9RamOrmQR5gpGIRhWJM1w0EtmuQ1io=
github.com/shenwei356/stable v0.1.2 h1:TCpfL8bFvZxbZcCm6XaSXpKYv4UopnRejIx6f+StiuM=
github.com/shenwei356/stable v0.1.2/go.mod h1:KghgqlviHPiKn9AuSTpadb7ep74n42VsNtPLoZZ/JIc=
-github.com/shenwei356/util v0.5.2 h1:kU9bnkE3RRUAlya+hbfwy83iTMOJqIHOlYgejYPb7mU=
-github.com/shenwei356/util v0.5.2/go.mod h1:3tRAOfreWdgl/Zh1gE008h2lWocf5/YAxVSjgLKvd4k=
+github.com/shenwei356/util v0.5.3 h1:Yf9+rB3Kngnb4+K3xCo7Dg2d+C1CzGsWmv6L9aDFORg=
+github.com/shenwei356/util v0.5.3/go.mod h1:3tRAOfreWdgl/Zh1gE008h2lWocf5/YAxVSjgLKvd4k=
github.com/shenwei356/xopen v0.3.2 h1:gD/0EvcMa6m2Y1XSdALs9WdhIgiZmn5wVZTjKldCCQo=
github.com/shenwei356/xopen v0.3.2/go.mod h1:6EQUa6I7Zsl2GQKqcL9qGLrTzVE+oZyly+uhzovQYSk=
github.com/smallfish/simpleyaml v0.1.0 h1:5uAZdLAiHxS9cmzkOxg7lH0dILXKTD7uRZbAhyHmyU0=
=====================================
seqkit/cmd/grep.go
=====================================
@@ -471,6 +471,9 @@ Examples:
}
if limitRegion {
target = sequence.SubSeq(start, end).Seq
+ if len(target) == 0 {
+ continue
+ }
} else if circular {
// concat two copies of sequence, and do not change orginal sequence
target = make([]byte, len(sequence.Seq)*2)
@@ -607,6 +610,9 @@ Examples:
}
if limitRegion {
target = sequence.SubSeq(start, end).Seq
+ if len(target) == 0 {
+ continue
+ }
} else if circular {
// concat two copies of sequence, and do not change orginal sequence
target = make([]byte, len(sequence.Seq)*2)
=====================================
seqkit/cmd/helper.go
=====================================
@@ -99,7 +99,7 @@ func getFileListFromFile(file string, checkFile bool) ([]string, error) {
return nil, fmt.Errorf("read file list from '%s': %s", file, err)
}
- return lists, nil
+ return lists, fh.Close()
}
func getFileListFromArgsAndFile(cmd *cobra.Command, args []string, checkFileFromArgs bool, flag string, checkFileFromFile bool) []string {
=====================================
seqkit/cmd/locate.go
=====================================
@@ -857,7 +857,7 @@ Attention:
// }
if nonGreedy {
- offset = offset + loc[1] + 1
+ offset = offset + loc[1]
} else {
offset = offset + loc[0] + 1
}
@@ -956,7 +956,7 @@ Attention:
// }
if nonGreedy {
- offset = offset + loc[1] + 1
+ offset = offset + loc[1]
} else {
offset = offset + loc[0] + 1
}
=====================================
seqkit/cmd/replace.go
=====================================
@@ -24,6 +24,7 @@ import (
"bytes"
"fmt"
"io"
+ "path/filepath"
"regexp"
"runtime"
"strings"
@@ -61,6 +62,9 @@ more on: http://bioinf.shenwei.me/seqkit/usage/#replace
Special replacement symbols (only for replacing name not sequence):
{nr} Record number, starting from 1
+ {fn} File name
+ {fbn} File base name
+ {fbne} File base name without any extension
{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)
@@ -132,6 +136,21 @@ Filtering records to edit:
replaceWithNR = true
}
+ var replaceWithFN bool
+ if reFN.Match(replacement) {
+ replaceWithFN = true
+ }
+
+ var replaceWithFBN bool
+ if reFBN.Match(replacement) {
+ replaceWithFBN = true
+ }
+
+ var replaceWithFBNE bool
+ if reFN.Match(replacement) {
+ replaceWithFBNE = true
+ }
+
var replaceWithKV bool
var kvs map[string]string
if reKV.Match(replacement) {
@@ -328,10 +347,23 @@ Filtering records to edit:
var re *regexp.Regexp
var h uint64
+ var fileBase string
+
for _, file := range files {
fastxReader, err := fastx.NewReader(alphabet, file, idRegexp)
checkError(err)
+
nr := 0
+ bFile := []byte(file)
+ fileBase = filepath.Base(file)
+ bFileBase := []byte(fileBase)
+ var bFileBaseWithoutExtension []byte
+ if i := strings.Index(fileBase, "."); i >= 0 {
+ bFileBaseWithoutExtension = []byte(fileBase[:i])
+ } else {
+ bFileBaseWithoutExtension = []byte(fileBase)
+ }
+
for {
record, err = fastxReader.Read()
if err != nil {
@@ -429,6 +461,16 @@ Filtering records to edit:
r = reNR.ReplaceAll(r, []byte(fmt.Sprintf(nrFormat, nr)))
}
+ if replaceWithFN {
+ r = reFN.ReplaceAll(r, bFile)
+ }
+ if replaceWithFBN {
+ r = reFBN.ReplaceAll(r, bFileBase)
+ }
+ if replaceWithFBNE {
+ r = reFBNE.ReplaceAll(r, bFileBaseWithoutExtension)
+ }
+
if replaceWithKV {
founds = patternRegexp.FindAllSubmatch(record.Name, -1)
if len(founds) > 1 {
@@ -483,7 +525,7 @@ func init() {
"replacement. supporting capture variables. "+
" e.g. $1 represents the text of the first submatch. "+
"ATTENTION: for *nix OS, use SINGLE quote NOT double quotes or "+
- `use the \ escape character. Record number is also supported by "{nr}".`+
+ `use the \ escape character. Record number and file name is also supported by "{nr}" and "{fn}".`+
`use ${1} instead of $1 when {kv} given!`)
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")
@@ -508,3 +550,6 @@ func init() {
var reNR = regexp.MustCompile(`\{(NR|nr)\}`)
var reKV = regexp.MustCompile(`\{(KV|kv)\}`)
+var reFN = regexp.MustCompile(`\{(FN|fn)\}`)
+var reFBN = regexp.MustCompile(`\{(FBN|fbn)\}`)
+var reFBNE = regexp.MustCompile(`\{(FBNE|fbne)\}`)
=====================================
seqkit/cmd/stat.go
=====================================
@@ -76,6 +76,7 @@ Columns:
16. Q30(%) percentage of bases with the quality score greater than 30
17. AvgQual average quality
18. GC(%) percentage of GC content
+ 19. sum_n number of ambitious letters (N, n, X, x)
Attention:
1. Sequence length metrics (sum_len, min_len, avg_len, max_len, Q1, Q2, Q3)
@@ -109,6 +110,7 @@ Tips:
}
gapLettersBytes := []byte(gapLetters)
gcLettersBytes := []byte{'g', 'c', 'G', 'C'}
+ nLettersBytes := []byte{'X', 'x', 'N', 'n'}
skipFileCheck := getFlagBool(cmd, "skip-file-check")
all := getFlagBool(cmd, "all")
@@ -194,7 +196,7 @@ Tips:
"max_len",
}
if all {
- colnames = append(colnames, []string{"Q1", "Q2", "Q3", "sum_gap", "N50", "N50_num", "Q20(%)", "Q30(%)", "AvgQual", "GC(%)"}...)
+ colnames = append(colnames, []string{"Q1", "Q2", "Q3", "sum_gap", "N50", "N50_num", "Q20(%)", "Q30(%)", "AvgQual", "GC(%)", "sum_n"}...)
}
if hasNX {
@@ -242,7 +244,7 @@ Tips:
info.lenAvg,
info.lenMax)
if all {
- fmt.Fprintf(outfh, "\t%.1f\t%.1f\t%.1f\t%d\t%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f",
+ fmt.Fprintf(outfh, "\t%.1f\t%.1f\t%.1f\t%d\t%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%d",
info.Q1,
info.Q2,
info.Q3,
@@ -252,7 +254,9 @@ Tips:
info.q20,
info.q30,
info.avgQual,
- info.gc)
+ info.gc,
+ info.nSum,
+ )
}
if hasNX {
for _, x = range info.nx {
@@ -283,7 +287,7 @@ Tips:
info.lenAvg,
info.lenMax)
if all {
- fmt.Fprintf(outfh, "\t%.1f\t%.1f\t%.1f\t%d\t%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f",
+ fmt.Fprintf(outfh, "\t%.1f\t%.1f\t%.1f\t%d\t%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%d",
info.Q1,
info.Q2,
info.Q3,
@@ -293,7 +297,9 @@ Tips:
info.q20,
info.q30,
info.avgQual,
- info.gc)
+ info.gc,
+ info.nSum,
+ )
}
if hasNX {
for _, x = range info.nx {
@@ -332,7 +338,7 @@ Tips:
info.lenAvg,
info.lenMax)
if all {
- fmt.Fprintf(outfh, "\t%.1f\t%.1f\t%.1f\t%d\t%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f",
+ fmt.Fprintf(outfh, "\t%.1f\t%.1f\t%.1f\t%d\t%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%d",
info.Q1,
info.Q2,
info.Q3,
@@ -342,7 +348,9 @@ Tips:
info.q20,
info.q30,
info.avgQual,
- info.gc)
+ info.gc,
+ info.nSum,
+ )
}
if hasNX {
for _, x = range info.nx {
@@ -400,6 +408,7 @@ Tips:
var gapSum uint64
var gcSum uint64
+ var nSum uint64
lensStats := util.NewLengthStats()
@@ -478,6 +487,7 @@ Tips:
gapSum += uint64(byteutil.CountBytes(record.Seq.Seq, gapLettersBytes))
gcSum += uint64(byteutil.CountBytes(record.Seq.Seq, gcLettersBytes))
+ nSum += uint64(byteutil.CountBytes(record.Seq.Seq, nLettersBytes))
}
}
@@ -528,7 +538,7 @@ Tips:
file = stdinLabel
}
ch <- statInfo{file, seqFormat, t,
- 0, 0, 0, 0,
+ 0, 0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0,
0, 0, 0, 0,
@@ -542,7 +552,7 @@ Tips:
file = stdinLabel
}
ch <- statInfo{file, seqFormat, t,
- lensStats.Count(), lensStats.Sum(), gapSum, lensStats.Min(),
+ lensStats.Count(), lensStats.Sum(), gapSum, lensStats.Min(), nSum,
mathutil.Round(lensStats.Mean(), 1), lensStats.Max(), n50, l50,
q1, q2, q3,
mathutil.Round(float64(q20)/float64(lensStats.Sum())*100, 2),
@@ -601,6 +611,7 @@ Tips:
{Header: "Q30(%)", Align: stable.AlignRight, HumanizeNumbers: true},
{Header: "AvgQual", Align: stable.AlignRight, HumanizeNumbers: true},
{Header: "GC(%)", Align: stable.AlignRight, HumanizeNumbers: true},
+ {Header: "sum_n", Align: stable.AlignRight, HumanizeNumbers: true},
// {Header: "L50", AlignRight: true},
}...)
}
@@ -634,6 +645,7 @@ Tips:
row = append(row, info.q30)
row = append(row, info.avgQual)
row = append(row, info.gc)
+ row = append(row, info.nSum)
}
if hasNX {
for _, x = range info.nx {
@@ -656,6 +668,7 @@ type statInfo struct {
lenSum uint64
gapSum uint64
lenMin uint64
+ nSum uint64
lenAvg float64
lenMax uint64
=====================================
seqkit/cmd/version.go
=====================================
@@ -29,7 +29,7 @@ import (
)
// VERSION of seqkit
-const VERSION = "2.8.2"
+const VERSION = "2.9.0"
// versionCmd represents the version command
var versionCmd = &cobra.Command{
=====================================
seqkit/packaging.sh
=====================================
@@ -17,3 +17,5 @@ for f in seqkit_*; do
rm -rf $f;
cd ..;
done;
+
+ls binaries/*.tar.gz | rush 'cd {/}; md5sum {%} > {%}.md5.txt'
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/0d9b2783790c2961740f2003b84f44d50f7bcd05...41d03f49b7514777d0afaf7d67a9f3f33b240b4b
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/0d9b2783790c2961740f2003b84f44d50f7bcd05...41d03f49b7514777d0afaf7d67a9f3f33b240b4b
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