[med-svn] [Git][med-team/seqkit][master] 6 commits: Fix watchfile to detect new versions on github
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Aug 25 17:21:07 BST 2022
Andreas Tille pushed to branch master at Debian Med / seqkit
Commits:
c75880f2 by Andreas Tille at 2022-08-25T18:15:48+02:00
Fix watchfile to detect new versions on github
- - - - -
2cfce477 by Andreas Tille at 2022-08-25T18:16:31+02:00
routine-update: New upstream version
- - - - -
f51e200a by Andreas Tille at 2022-08-25T18:16:32+02:00
New upstream version 2.3.0+ds
- - - - -
ec3f07b1 by Andreas Tille at 2022-08-25T18:16:46+02:00
Update upstream source from tag 'upstream/2.3.0+ds'
Update to upstream version '2.3.0+ds'
with Debian dir a993bf1ad9ad87111c5ea18661b11e4cc0f934f5
- - - - -
f0117f2c by Andreas Tille at 2022-08-25T18:16:53+02:00
Apply multi-arch hints.
+ seqkit-examples: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
- - - - -
50f12697 by Andreas Tille at 2022-08-25T18:19:25+02:00
routine-update: Ready to upload to unstable
- - - - -
20 changed files:
- .gitignore
- + .travis.yml
- CHANGELOG.md
- README.md
- debian/changelog
- debian/control
- debian/watch
- doc/docs/download.md
- doc/docs/usage.md
- go.mod
- go.sum
- seqkit/cmd/concat.go
- seqkit/cmd/grep.go
- seqkit/cmd/pair.go
- seqkit/cmd/rename.go
- seqkit/cmd/seq.go
- seqkit/cmd/split.go
- seqkit/cmd/split2.go
- seqkit/cmd/stat.go
- seqkit/cmd/version.go
Changes:
=====================================
.gitignore
=====================================
@@ -39,3 +39,4 @@ doc/docs/chinese/
dataset_A.fa*
dataset_B.fa*
dataset_C.fq*
+dataset_Ca.fq*
=====================================
.travis.yml
=====================================
@@ -0,0 +1,28 @@
+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
=====================================
@@ -1,7 +1,20 @@
+- [SeqKit v2.3.0](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0) - 2022-08-12
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0)
+ - `seqkit grep/rename`:
+ - *reduce memory comsumption for a lot of searching patterns, and it's faster*. [#305](https://github.com/shenwei356/seqkit/issues/305)
+ - 2X faster `-s/--by-seq`.
+ - `seqkit split`
+ - fix outputting an empty file when the number of sequence equal to the split size. [#293](https://github.com/shenwei356/seqkit/issues/293)
+ - add options to set output file prefix and extention. [#296](https://github.com/shenwei356/seqkit/issues/296)
+ - `seqkit split2`
+ - reduce memory consumption. [#304](https://github.com/shenwei356/seqkit/issues/304)
+ - add options to set output file prefix
+ - `seqkit stats`:
+ - add GC content. [#294](https://github.com/shenwei356/seqkit/issues/294)
- [SeqKit v2.2.0](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0) - 2022-03-14
[](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0)
- `seqkit`:
- - **add support of `zx` and `zstd` input/output formats**. [#274](https://github.com/shenwei356/seqkit/issues/274)
+ - **add support of `xz` and `zstd` input/output formats**. [#274](https://github.com/shenwei356/seqkit/issues/274)
- fix panic when reading records with header of `ID` + blanks.
- **new command `seqkit sum`: computing message digest for all sequences in FASTA/Q files**.
The idea comes from @photocyte and the format borrows from [seqhash](https://github.com/TimothyStiles/poly/tree/prime/seqhash) [#262](https://github.com/shenwei356/seqkit/issues/262)
=====================================
README.md
=====================================
@@ -16,7 +16,7 @@ and
[](http://bioinf.shenwei.me/seqkit/download/)
[](https://anaconda.org/bioconda/seqkit)
- **[Please cite](#citation):** [](https://doi.org/10.1371/journal.pone.0163962)
-<span class="__dimensions_badge_embed__" data-doi="10.1371/journal.pone.0163962" data-style="small_rectangle"></span>
+[](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)
## Features
@@ -46,9 +46,9 @@ install via conda:
|category |command |function |input |strand-sensitivity|multi-threads|popularity |
|:----------------|:------------------------------------------------------------------|:---------------------------------------------------------------------------------------|:--------------|:-----------------|:------------|:--------------|
-|basic |[seq](https://bioinf.shenwei.me/seqkit/usage/#seq) |transform sequences: extract ID/seq, filter by length/quality, remove gaps… |FASTA/Q | | |★★★★★ |
+|basic |[seq](https://bioinf.shenwei.me/seqkit/usage/#seq) |transform sequences: extract ID/seq, filter by length/quality, remove gaps, reverse complement… |FASTA/Q | | |★★★★★ |
| |[stats](https://bioinf.shenwei.me/seqkit/usage/#stats) |simple statistics: #seqs, min/max_len, N50, Q20%, Q30%… |FASTA/Q | |✓ |★★★★★ |
-| |[sum](https://bioinf.shenwei.me/seqkit/usage/sum) |compute message digest for all sequences in FASTA/Q files |FASTA/Q |+ or both |✓ | |
+| |[sum](https://bioinf.shenwei.me/seqkit/usage/#sum) |compute message digest for all sequences in FASTA/Q files |FASTA/Q |+ or both |✓ | |
| |[subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) |extract subsequences or flanking sequences by region/gtf/bed, |FASTA/Q |+ or/and - | |★★★ |
| |[sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding) |extract subsequences in sliding windows |FASTA/Q |+ only | |★★ |
| |[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx) |create FASTA index file and extract subsequence (with more features than samtools faidx)|FASTA |+ or/and - | | |
@@ -140,4 +140,3 @@ propose new functions or ask for help.
<img src="https://starchart.cc/shenwei356/seqkit.svg" alt="Stargazers over time" style="max-width: 100%">
-<script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+seqkit (2.3.0+ds-1) unstable; urgency=medium
+
+ * Fix watchfile to detect new versions on github
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Thu, 25 Aug 2022 18:16:54 +0200
+
seqkit (2.2.0+ds-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -52,6 +52,7 @@ Package: seqkit-examples
Architecture: all
Depends: ${misc:Depends},
${shlibs:Depends}
+Multi-Arch: foreign
Description: examples for seqkit: toolkit for FASTA/Q file manipulation
SeqKit describes a cross-platform ultrafast comprehensive toolkit for
FASTA/Q processing. SeqKit provides executable binary files for all
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%,uversionmangle=s/rc/~rc/,repacksuffix=+ds,dversionmangle=auto" \
-https://github.com/shenwei356/seqkit/releases .*/archive/.*/v?@ANY_VERSION@\.tar\.gz
+https://github.com/shenwei356/seqkit/releases .*/.*/v?@ANY_VERSION@\.tar\.gz
=====================================
doc/docs/download.md
=====================================
@@ -5,23 +5,35 @@ statically-linked executable binary files are [freely available](https://github.
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).
+[](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=wHF3Lm8AAAAJ&citation_for_view=wHF3Lm8AAAAJ:zYLM7Y9cAGgC)
## Current Version
-- [SeqKit v2.2.0](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0) - 2022-03-14
-[](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0)
-
+- [SeqKit v2.3.0](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0) - 2022-08-12
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0)
+ - `seqkit grep/rename`:
+ - *reduce memory comsumption for a lot of searching patterns, and it's faster*. [#305](https://github.com/shenwei356/seqkit/issues/305)
+ - 2X faster `-s/--by-seq`.
+ - `seqkit split`
+ - fix outputting an empty file when the number of sequence equal to the split size. [#293](https://github.com/shenwei356/seqkit/issues/293)
+ - add options to set output file prefix and extention. [#296](https://github.com/shenwei356/seqkit/issues/296)
+ - `seqkit split2`
+ - reduce memory consumption. [#304](https://github.com/shenwei356/seqkit/issues/304)
+ - add options to set output file prefix
+ - `seqkit stats`:
+ - add GC content. [#294](https://github.com/shenwei356/seqkit/issues/294)
+
### Links
OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.2.0/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/v2.2.0/seqkit_linux_386.tar.gz)
-Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.2.0/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/v2.2.0/seqkit_linux_amd64.tar.gz)
-Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.2.0/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/v2.2.0/seqkit_linux_arm64.tar.gz)
-macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.2.0/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/v2.2.0/seqkit_darwin_amd64.tar.gz)
-macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.2.0/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/v2.2.0/seqkit_darwin_arm64.tar.gz)
-Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.2.0/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/v2.2.0/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.2.0/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/v2.2.0/seqkit_windows_amd64.exe.tar.gz)
+Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_linux_386.tar.gz)
+Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_linux_amd64.tar.gz)
+Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_linux_arm64.tar.gz)
+macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_darwin_amd64.tar.gz)
+macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_windows_amd64.exe.tar.gz)
*Notes*
@@ -75,6 +87,44 @@ Run the following commands:
cd seqkit
docker build -t shenwei356/seqkit .
docker run -it shenwei356/seqkit:latest
+
+#### Method 6: Compiling from source (latest stable/dev version)
+
+ # ------------------- install golang -----------------
+
+ # download Go from https://go.dev/dl
+ wget https://go.dev/dl/go1.17.13.linux-amd64.tar.gz
+
+ tar -zxf go1.17.13.linux-amd64.tar.gz -C $HOME/
+
+ # or
+ # echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc
+ # source ~/.bashrc
+ export PATH=$PATH:$HOME/go/bin
+
+
+ # ------------- the latest stable version -------------
+
+ go get -v -u github.com/shenwei356/seqkit/seqkit
+
+ # The executable binary file is located in:
+ # ~/go/bin/seqkit
+ # You can also move it to anywhere in the $PATH
+ mkdir -p $HOME/bin
+ cp ~/go/bin/seqkit $HOME/bin/
+
+ # --------------- the devlopment version --------------
+
+ git clone https://github.com/shenwei356/seqkit
+ cd seqkit/seqkit/
+ go build
+
+ # The executable binary file is located in:
+ # ./seqkit
+ # You can also move it to anywhere in the $PATH
+ mkdir -p $HOME/bin
+ cp ./seqkit $HOME/bin/
+
## Shell-completion
@@ -108,7 +158,7 @@ fish:
- [SeqKit v2.2.0](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0) - 2020-03-14
[](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0)
- `seqkit`:
- - **add support of `zx` and `zstd` input/output formats**. [#274](https://github.com/shenwei356/seqkit/issues/274)
+ - **add support of `xz` and `zstd` input/output formats**. [#274](https://github.com/shenwei356/seqkit/issues/274)
- fix panic when reading records with header of `ID` + blanks.
- **new command `seqkit sum`: computing message digest for all sequences in FASTA/Q files**.
The idea comes from @photocyte and the format borrows from [seqhash](https://github.com/TimothyStiles/poly/tree/prime/seqhash) [#262](https://github.com/shenwei356/seqkit/issues/262)
=====================================
doc/docs/usage.md
=====================================
@@ -156,7 +156,7 @@ reproduced in different environments with same random seed.
``` text
SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
-Version: 2.2.0
+Version: 2.3.0
Author: Wei Shen <shenwei356 at gmail.com>
@@ -272,7 +272,7 @@ Only DNA and gtf/bed data of Chr1 were used:
Usage
``` text
-transform sequences (extract ID, filter by length, remove gaps...)
+transform sequences (extract ID, filter by length, remove gaps, reverse complement...)
Usage:
seqkit seq [flags]
@@ -703,12 +703,13 @@ 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 Q20(%) Q30(%)
- hairpin.fa.gz FASTA RNA 28,645 2,949,871 39 103 2,354 76 91 111 0 101 0 0
- mature.fa.gz FASTA RNA 35,828 781,222 15 21.8 34 21 22 22 0 22 0 0
- Illimina1.8.fq.gz FASTQ DNA 10,000 1,500,000 150 150 150 150 150 150 0 150 96.16 89.71
- reads_1.fq.gz FASTQ DNA 2,500 567,516 226 227 229 227 227 227 0 227 91.24 86.62
- reads_2.fq.gz FASTQ DNA 2,500 560,002 223 224 225 224 224 224 0 224 91.06 87.66
+ file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 Q20(%) Q30(%) GC(%)
+ hairpin.fa.gz FASTA RNA 28,645 2,949,871 39 103 2,354 76 91 111 0 101 0 0 45.77
+ mature.fa.gz FASTA RNA 35,828 781,222 15 21.8 34 21 22 22 0 22 0 0 47.6
+ Illimina1.8.fq.gz FASTQ DNA 10,000 1,500,000 150 150 150 75 150 75 0 150 96.16 89.71 49.91
+ nanopore.fq.gz FASTQ DNA 4,000 1,798,723 153 449.7 6,006 271 318 391 0 395 40.79 12.63 46.66
+ reads_1.fq.gz FASTQ DNA 2,500 567,516 226 227 229 227 227 227 0 227 91.24 86.62 53.63
+ reads_2.fq.gz FASTQ DNA 2,500 560,002 223 224 225 224 224 224 0 224 91.06 87.66 54.77
1. **Parallelize counting files, it's much faster for lots of small files, especially for files on SSD**
@@ -1612,7 +1613,7 @@ Examples
1. Just print the matched number, like GNU grep (`grep -c`)
- $ seqkit grep -f id.txt seqs.fq.gz -C
+ $ seqkit grep -f id.txt seqs.fq.gz -C
1. Serching non-canonical sequence IDs, Using `--id-regexp` to capture IDs.
Refer to [section Sequence ID](#sequence-id) and [seqkit seq](#seq) for examples.
@@ -2287,7 +2288,7 @@ split sequences into files by name ID, subsequence of given region,
part size or number of parts.
If you just want to split by parts or sizes, please use "seqkit split2",
-which also apply for paired- and single-end FASTQ.
+which also applies for paired- and single-end FASTQ.
The definition of region is 1-based and with some custom design.
@@ -2310,16 +2311,21 @@ Usage:
seqkit split [flags]
Flags:
- -i, --by-id split squences according to sequence ID
- -p, --by-part int split sequences into N parts
- -r, --by-region string split squences according to subsequence of given region. e.g 1:12 for first 12 bases, -12:-1 for last 12 bases. type "seqkit split -h" for more examples
- -s, --by-size int split sequences into multi parts with N sequences
- -d, --dry-run dry run, just print message and no files will be created.
- -f, --force overwrite output directory
- -h, --help help for split
- -k, --keep-temp keep tempory FASTA and .fai file when using 2-pass mode
- -O, --out-dir string output directory (default value is $infile.split)
- -2, --two-pass two-pass mode read files twice to lower memory usage. (only for FASTA format)
+ -i, --by-id split squences according to sequence ID
+ --by-id-prefix string file prefix for --by-id
+ -p, --by-part int split sequences into N parts
+ --by-part-prefix string file prefix for --by-part
+ -r, --by-region string split squences according to subsequence of given region. e.g 1:12 for first 12 bases, -12:-1 for last 12 bases. type "seqkit split -h" for more examples
+ --by-region-prefix string file prefix for --by-region
+ -s, --by-size int split sequences into multi parts with N sequences
+ --by-size-prefix string file prefix for --by-size
+ -d, --dry-run dry run, just print message and no files will be created.
+ -e, --extension string set output file extension, e.g., ".gz", ".xz", or ".zst"
+ -f, --force overwrite output directory
+ -h, --help help for split
+ -k, --keep-temp keep temporary FASTA and .fai file when using 2-pass mode
+ -O, --out-dir string output directory (default value is $infile.split)
+ -2, --two-pass two-pass mode read files twice to lower memory usage. (only for FASTA format)
```
@@ -2413,15 +2419,18 @@ Usage:
seqkit split2 [flags]
Flags:
- -l, --by-length string split sequences into chunks of >=N bases, supports K/M/G suffix
- -p, --by-part int split sequences into N parts
- -s, --by-size int split sequences into multi parts with N sequences
- -e, --extension string set output file extension, e.g., ".gz", ".xz", or ".zst"
- -f, --force overwrite output directory
- -h, --help help for split2
- -O, --out-dir string output directory (default value is $infile.split)
- -1, --read1 string (gzipped) read1 file
- -2, --read2 string (gzipped) read2 file
+ -l, --by-length string split sequences into chunks of >=N bases, supports K/M/G suffix
+ --by-length-prefix string file prefix for --by-length
+ -p, --by-part int split sequences into N parts
+ --by-part-prefix string file prefix for --by-part
+ -s, --by-size int split sequences into multi parts with N sequences
+ --by-size-prefix string file prefix for --by-size
+ -e, --extension string set output file extension, e.g., ".gz", ".xz", or ".zst"
+ -f, --force overwrite output directory
+ -h, --help help for split2
+ -O, --out-dir string output directory (default value is $infile.split)
+ -1, --read1 string (gzipped) read1 file
+ -2, --read2 string (gzipped) read2 file
```
Examples
@@ -2521,15 +2530,15 @@ Usage
```text
match up paired-end reads from two fastq files
-Attensions:
+Attentions:
1. Orders of headers in the two files better be the same (not shuffled),
- otherwise it consumes huge number of memory for buffering reads in memory.
+ otherwise, it consumes a huge number of memory for buffering reads in memory.
2. Unpaired reads are optional outputted with the flag -u/--save-unpaired.
-3. If the flag -O/--out-dir not given, output will be saved in the same directory
- of input, with suffix "paired", e.g., read_1.paired.fq.gz.
- Otherwise names are kept untouched in the given output directory.
+3. If the flag -O/--out-dir is not given, the output will be saved in the same directory
+ of input, with the suffix "paired", e.g., read_1.paired.fq.gz.
+ Otherwise, names are kept untouched in the given output directory.
4. Paired gzipped files may be slightly larger than original files, because
- of using different gzip package/library, don't worry.
+ of using a different gzip package/library, don't worry.
Usage:
seqkit pair [flags]
@@ -3056,7 +3065,7 @@ Aliases:
concat, concate
Flags:
- -f, --full keep all sequences, like full/outter join
+ -f, --full keep all sequences, like full/outer join
-h, --help help for concat
-s, --separator string separator for descriptions of records with the same ID (default "|")
=====================================
go.mod
=====================================
@@ -11,7 +11,7 @@ require (
github.com/dustin/go-humanize v1.0.0
github.com/fsnotify/fsnotify v1.5.1
github.com/iafan/cwalk v0.0.0-20210125030640-586a8832a711
- github.com/klauspost/compress v1.15.1
+ github.com/klauspost/compress v1.15.8
github.com/klauspost/pgzip v1.2.5
github.com/logrusorgru/aurora v2.0.3+incompatible
github.com/mattn/go-colorable v0.1.11
@@ -19,11 +19,11 @@ require (
github.com/mitchellh/go-homedir v1.1.0
github.com/pkg/errors v0.9.1
github.com/shenwei356/bio v0.7.0
- github.com/shenwei356/breader v0.3.1
+ github.com/shenwei356/breader v0.3.2
github.com/shenwei356/bwt v0.6.0
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
github.com/shenwei356/util v0.5.0
- github.com/shenwei356/xopen v0.2.1
+ github.com/shenwei356/xopen v0.2.2
github.com/smallfish/simpleyaml v0.1.0
github.com/spf13/cobra v1.4.0
github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939
=====================================
go.sum
=====================================
@@ -1,51 +1,7 @@
-cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
-cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
-cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU=
-cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU=
-cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY=
-cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc=
-cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0=
-cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To=
-cloud.google.com/go v0.52.0/go.mod h1:pXajvRH/6o3+F9jDHZWQ5PbGhn+o8w9qiu/CffaVdO4=
-cloud.google.com/go v0.53.0/go.mod h1:fp/UouUEsRkN6ryDKNW/Upv/JBKnv6WDthjR6+vze6M=
-cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc=
-cloud.google.com/go v0.56.0/go.mod h1:jr7tqZxxKOVYizybht9+26Z/gUq7tiRzu+ACVAMbKVk=
-cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs=
-cloud.google.com/go v0.62.0/go.mod h1:jmCYTdRCQuc1PHIIJ/maLInMho30T/Y0M4hTdTShOYc=
-cloud.google.com/go v0.65.0/go.mod h1:O5N8zS7uWy9vkA9vayVHs65eM1ubvY4h553ofrNHObY=
-cloud.google.com/go v0.72.0/go.mod h1:M+5Vjvlc2wnp6tjzE102Dw08nGShTscUx2nZMufOKPI=
-cloud.google.com/go v0.74.0/go.mod h1:VV1xSbzvo+9QJOxLDaJfTjx5e+MePCpCWwvftOeQmWk=
-cloud.google.com/go v0.78.0/go.mod h1:QjdrLG0uq+YwhjoVOLsS1t7TW8fs36kLs4XO5R5ECHg=
-cloud.google.com/go v0.79.0/go.mod h1:3bzgcEeQlzbuEAYu4mrWhKqWjmpprinYgKJLgKHnbb8=
-cloud.google.com/go v0.81.0/go.mod h1:mk/AM35KwGk/Nm2YSeZbxXdrNK3KZOYHmLkOqC2V6E0=
-cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o=
-cloud.google.com/go/bigquery v1.3.0/go.mod h1:PjpwJnslEMmckchkHFfq+HTD2DmtT67aNFKH1/VBDHE=
-cloud.google.com/go/bigquery v1.4.0/go.mod h1:S8dzgnTigyfTmLBfrtrhyYhwRxG72rYxvftPBK2Dvzc=
-cloud.google.com/go/bigquery v1.5.0/go.mod h1:snEHRnqQbz117VIFhE8bmtwIDY80NLUZUMb4Nv6dBIg=
-cloud.google.com/go/bigquery v1.7.0/go.mod h1://okPTzCYNXSlb24MZs83e2Do+h+VXtc4gLoIoXIAPc=
-cloud.google.com/go/bigquery v1.8.0/go.mod h1:J5hqkt3O0uAFnINi6JXValWIb1v0goeZM77hZzJN/fQ=
-cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE=
-cloud.google.com/go/datastore v1.1.0/go.mod h1:umbIZjpQpHh4hmRpGhH4tLFup+FVzqBi1b3c64qFpCk=
-cloud.google.com/go/firestore v1.1.0/go.mod h1:ulACoGHTpvq5r8rxGJ4ddJZBZqakUQqClKRT5SZwBmk=
-cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I=
-cloud.google.com/go/pubsub v1.1.0/go.mod h1:EwwdRX2sKPjnvnqCa270oGRyludottCI76h+R3AArQw=
-cloud.google.com/go/pubsub v1.2.0/go.mod h1:jhfEVHT8odbXTkndysNHCcx0awwzvfOlguIAii9o8iA=
-cloud.google.com/go/pubsub v1.3.1/go.mod h1:i+ucay31+CNRpDW4Lu78I4xXG+O1r/MAHgjpRVR+TSU=
-cloud.google.com/go/storage v1.0.0/go.mod h1:IhtSnM/ZTZV8YYJWCY8RULGVqBDmpoyjwiyrjsg+URw=
-cloud.google.com/go/storage v1.5.0/go.mod h1:tpKbwo567HUNpVclU5sGELwQWBDZ8gh0ZeosJ0Rtdos=
-cloud.google.com/go/storage v1.6.0/go.mod h1:N7U0C8pVQ/+NIKOBQyamJIeKQKkZ+mxpohlUTyfDhBk=
-cloud.google.com/go/storage v1.8.0/go.mod h1:Wv1Oy7z6Yz3DshWRJFhqM/UCfaWIRTdp0RXyy7KQOVs=
-cloud.google.com/go/storage v1.10.0/go.mod h1:FLPqc6j+Ki4BU591ie1oL6qBQGu2Bl/tZ9ullr3+Kg0=
dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
-github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af h1:wVe6/Ea46ZMeNkQjjBW6xcqyQA/j5e0D6GytH95g0gQ=
github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw=
-github.com/antihax/optional v1.0.0/go.mod h1:uupD/76wgC+ih3iEmQUL+0Ugr19nfwCT1kdvxnR2qWY=
-github.com/armon/circbuf v0.0.0-20150827004946-bbbad097214e/go.mod h1:3U/XgcO3hCbHZ8TKRvWD2dDTCfh9M9ya+I9JpbB7O8o=
-github.com/armon/go-metrics v0.0.0-20180917152333-f0300d1749da/go.mod h1:Q73ZrmVTwzkszR9V5SSuryQ31EELlFMUz1kKyl939pY=
-github.com/armon/go-radix v0.0.0-20180808171621-7fddfc383310/go.mod h1:ufUuZ+zHj4x4TnLV4JWEpy2hxWSpsRywHrMgIH9cCH8=
-github.com/bgentry/speakeasy v0.1.0/go.mod h1:+zsyZBPWlz7T6j88CTgSN5bM796AkVf0kBD4zp0CCIs=
github.com/biogo/biogo v1.0.3 h1:LSRUaHBW5WyyTBkfG9lGZOych6uvfbFPB9j9OLaZ7Nw=
github.com/biogo/biogo v1.0.3/go.mod h1:WlqzR+oIOt6UKRqDbDsbLm7zHe4+FLLDd9iFTrnfloc=
github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1 h1:LAHY5JxqhOgJDeDBGKsQ4300qd3sG8C0j5CQS8gD+Kw=
@@ -55,25 +11,12 @@ github.com/biogo/hts v1.1.0/go.mod h1:6C9MdMt9ALD5PsluK5n0B0svHOpmVse3UjQQx/cTgO
github.com/biogo/hts v1.4.3 h1:vir2yUTiRkPvtp6ZTpzh9lWTKQJZXJKZ563rpAQAsRM=
github.com/biogo/hts v1.4.3/go.mod h1:eW40HJ1l2ExK9C+yvvoRSftInqWsf3ue+zAEjzCGWjA=
github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83/go.mod h1:wdbXg77soR6ESRprAMEwAQDFtLT6EAGF5o1GRy0cB5k=
-github.com/bketelsen/crypt v0.0.4/go.mod h1:aI6NrJ0pMGgvZKL1iVgXLnfIFJtfV+bKCoqOes/6LfM=
github.com/bsipos/thist v1.0.0 h1:vZ3W5/ZnT54s4LHeonTCbnzCb20ERlJUnhiwXoGpsbY=
github.com/bsipos/thist v1.0.0/go.mod h1:7i0xwRua1/bmUxcxi2xAxaFL895rLtOpKUwnw3NrT8I=
-github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU=
github.com/cespare/xxhash/v2 v2.1.2 h1:YRXhKfTDauu4ajMg1TPgFO5jnlC2HCbmLXMcTG5cbYE=
github.com/cespare/xxhash/v2 v2.1.2/go.mod h1:VGX0DQ3Q6kWi7AoAeZDth3/j3BFtOZR5XLFGgcrjCOs=
-github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI=
-github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e/go.mod h1:nSuG5e5PlCu98SY8svDHJxuZscDgtXS6KTTbou5AhLI=
-github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU=
-github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw=
-github.com/cncf/udpa/go v0.0.0-20191209042840-269d4d468f6f/go.mod h1:M8M6+tZqaGXZJjfX53e64911xZQV5JYwmTeXPW+k8Sc=
-github.com/cncf/udpa/go v0.0.0-20200629203442-efcf912fb354/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk=
-github.com/cncf/udpa/go v0.0.0-20201120205902-5459f2c99403/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk=
-github.com/coreos/go-semver v0.3.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk=
-github.com/coreos/go-systemd/v22 v22.3.2/go.mod h1:Y58oyj3AT4RCenI/lSvhwexgC+NSVTIJ3seZv2GcEnc=
-github.com/cpuguy83/go-md2man/v2 v2.0.0/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU=
github.com/cpuguy83/go-md2man/v2 v2.0.1/go.mod h1:tgQtvFlXSQOSOSIRvRPT7W67SCa46tRHOmNcaadrF8o=
github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 h1:iwZdTE0PVqJCos1vaoKsclOGD3ADKpshg3SRtYBbwso=
-github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548/go.mod h1:e6NPNENfs9mPDVNRekM7lKScauxd5kXTr1Mfyig6TDM=
github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8 h1:LpMLYGyy67BoAFGda1NeOBQwqlv7nUXpm+rIVHGxZZ4=
github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8/go.mod h1:q2w6Bg5jeox1B+QkJ6Wp/+Vn0G/bo3f1uY7Fn3vivIQ=
github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
@@ -83,223 +26,71 @@ github.com/dustin/go-humanize v1.0.0 h1:VSnTsYCnlFHaM2/igO1h6X3HA71jcobQuxemgkq4
github.com/dustin/go-humanize v1.0.0/go.mod h1:HtrtbFcZ19U5GC7JDqmcUSB87Iq5E25KnS6fMYU6eOk=
github.com/edsrzf/mmap-go v1.0.0 h1:CEBF7HpRnUCSJgGUb5h1Gm7e3VkmVDrR8lvWVLtrOFw=
github.com/edsrzf/mmap-go v1.0.0/go.mod h1:YO35OhQPt3KJa3ryjFM5Bs14WD66h8eGKpfaBNrHW5M=
-github.com/envoyproxy/go-control-plane v0.9.0/go.mod h1:YTl/9mNaCwkRvm6d1a2C3ymFceY/DCBVvsKhRF0iEA4=
-github.com/envoyproxy/go-control-plane v0.9.1-0.20191026205805-5f8ba28d4473/go.mod h1:YTl/9mNaCwkRvm6d1a2C3ymFceY/DCBVvsKhRF0iEA4=
-github.com/envoyproxy/go-control-plane v0.9.4/go.mod h1:6rpuAdCZL397s3pYoYcLgu1mIlRU8Am5FuJP05cCM98=
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-github.com/envoyproxy/go-control-plane v0.9.9-0.20201210154907-fd9021fe5dad/go.mod h1:cXg6YxExXjJnVBQHBLXeUAgxn2UodCpnH306RInaBQk=
-github.com/envoyproxy/go-control-plane v0.9.9-0.20210217033140-668b12f5399d/go.mod h1:cXg6YxExXjJnVBQHBLXeUAgxn2UodCpnH306RInaBQk=
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github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k=
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rsc.io/pdf v0.1.1 h1:k1MczvYDUvJBe93bYd7wrZLLUEcLZAuF824/I4e5Xr4=
rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4=
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=====================================
seqkit/cmd/concat.go
=====================================
@@ -242,7 +242,7 @@ Attentions:
func init() {
RootCmd.AddCommand(concateCmd)
- concateCmd.Flags().BoolP("full", "f", false, "keep all sequences, like full/outter join")
+ concateCmd.Flags().BoolP("full", "f", false, "keep all sequences, like full/outer join")
concateCmd.Flags().StringP("separator", "s", "|", "separator for descriptions of records with the same ID")
}
=====================================
seqkit/cmd/grep.go
=====================================
@@ -30,6 +30,7 @@ import (
"strings"
"sync"
+ "github.com/cespare/xxhash/v2"
"github.com/shenwei356/bwt"
"github.com/twotwotwo/sorts/sortutil"
@@ -182,7 +183,11 @@ Examples:
}
// prepare pattern
- patterns := make(map[string]*regexp.Regexp)
+ patternsR := make(map[uint64]*regexp.Regexp, 1<<10)
+ patternsN := make(map[uint64]interface{}, 1<<20)
+ // patternsS := make(map[string]interface{}, 1<<10)
+ patternsS := make([][]byte, 0, 16)
+
var pattern2seq *seq.Seq
var pbyte []byte
if patternFile != "" {
@@ -220,7 +225,7 @@ Examples:
}
r, err := regexp.Compile(p)
checkError(err)
- patterns[p] = r
+ patternsR[xxhash.Sum64String(p)] = r
} else if bySeq {
pbyte = []byte(p)
if mismatches > 0 && mismatches > len(p) {
@@ -230,27 +235,29 @@ Examples:
seq.RNAredundant.IsValid(pbyte) == nil ||
seq.Protein.IsValid(pbyte) == nil { // legal sequence
if ignoreCase {
- patterns[strings.ToLower(p)] = nil
+ // patternsS[strings.ToLower(p)] = struct{}{}
+ patternsS = append(patternsS, bytes.ToLower(pbyte))
} else {
- patterns[p] = nil
+ // patternsS[p] = struct{}{}
+ patternsS = append(patternsS, pbyte)
}
} else {
checkError(fmt.Errorf("illegal DNA/RNA/Protein sequence: %s", p))
}
} else {
if ignoreCase {
- patterns[strings.ToLower(p)] = nil
+ patternsN[xxhash.Sum64String(strings.ToLower(p))] = struct{}{}
} else {
- patterns[p] = nil
+ patternsN[xxhash.Sum64String(p)] = struct{}{}
}
}
}
}
if !quiet {
- if len(patterns) == 0 {
- log.Warningf("%d patterns loaded from file", len(patterns))
+ if len(patternsR)+len(patternsN)+len(patternsS) == 0 {
+ log.Warningf("%d patterns loaded from file", 0)
} else {
- log.Infof("%d patterns loaded from file", len(patterns))
+ log.Infof("%d patterns loaded from file", len(patternsR)+len(patternsN)+len(patternsS))
}
}
} else {
@@ -278,7 +285,7 @@ Examples:
}
r, err := regexp.Compile(p)
checkError(err)
- patterns[p] = r
+ patternsR[xxhash.Sum64String(p)] = r
} else if bySeq {
pbyte = []byte(p)
if mismatches > 0 && mismatches > len(p) {
@@ -288,18 +295,20 @@ Examples:
seq.RNAredundant.IsValid(pbyte) == nil ||
seq.Protein.IsValid(pbyte) == nil { // legal sequence
if ignoreCase {
- patterns[strings.ToLower(p)] = nil
+ // patternsS[strings.ToLower(p)] = struct{}{}
+ patternsS = append(patternsS, bytes.ToLower(pbyte))
} else {
- patterns[p] = nil
+ // patternsS[p] = struct{}{}
+ patternsS = append(patternsS, pbyte)
}
} else {
checkError(fmt.Errorf("illegal DNA/RNA/Protein sequence: %s", p))
}
} else {
if ignoreCase {
- patterns[strings.ToLower(p)] = nil
+ patternsN[xxhash.Sum64String(strings.ToLower(p))] = struct{}{}
} else {
- patterns[p] = nil
+ patternsN[xxhash.Sum64String(p)] = struct{}{}
}
}
}
@@ -432,7 +441,8 @@ Examples:
var sequence *seq.Seq
var target []byte
var hit bool
- var k string
+ // var k string
+ var k []byte
sfmi := fmi.NewFMIndex()
@@ -468,8 +478,10 @@ Examples:
if err != nil {
checkError(fmt.Errorf("fail to build FMIndex for sequence: %s", record.Name))
}
- for k = range patterns {
- hit, err = sfmi.Match([]byte(k), mismatches)
+ // for k = range patternsS {
+ for _, k = range patternsS {
+ // hit, err = sfmi.Match([]byte(k), mismatches)
+ hit, err = sfmi.Match(k, mismatches)
if err != nil {
checkError(fmt.Errorf("fail to search pattern '%s' on seq '%s': %s", k, record.Name, err))
}
@@ -513,9 +525,10 @@ Examples:
var sequence *seq.Seq
var target []byte
var ok, hit bool
- var k string
+ // var k string
+ var k []byte
var re *regexp.Regexp
- var p string
+ var h uint64
var strand byte
for _, file := range files {
fastxReader, err = fastx.NewReader(alphabet, file, idRegexp)
@@ -587,11 +600,11 @@ Examples:
}
if degenerate || useRegexp {
- for p, re = range patterns {
+ for h, re = range patternsR {
if re.Match(target) {
hit = true
if deleteMatched && !invertMatch {
- delete(patterns, p)
+ delete(patternsR, h)
}
break
}
@@ -601,12 +614,14 @@ Examples:
target = bytes.ToLower(target)
}
if mismatches == 0 {
- for k = range patterns {
- if bytes.Contains(target, []byte(k)) {
+ // for k = range patternsS {
+ for _, k = range patternsS {
+ // if bytes.Contains(target, []byte(k)) {
+ if bytes.Contains(target, k) {
hit = true
- if deleteMatched && !invertMatch {
- delete(patterns, k)
- }
+ // if deleteMatched && !invertMatch {
+ // delete(patternsS, k)
+ // }
break
}
}
@@ -615,28 +630,27 @@ Examples:
if err != nil {
checkError(fmt.Errorf("fail to build FMIndex for sequence: %s", record.Name))
}
- for k = range patterns {
- hit, err = sfmi.Match([]byte(k), mismatches)
+ // for k = range patternsS {
+ for _, k = range patternsS {
+ // hit, err = sfmi.Match([]byte(k), mismatches)
+ hit, err = sfmi.Match(k, mismatches)
if err != nil {
checkError(fmt.Errorf("fail to search pattern '%s' on seq '%s': %s", k, record.Name, err))
}
if hit {
- if deleteMatched && !invertMatch {
- delete(patterns, k)
- }
break
}
}
}
} else {
- k = string(target)
+ h = xxhash.Sum64(target)
if ignoreCase {
- k = strings.ToLower(k)
+ h = xxhash.Sum64(bytes.ToLower(target))
}
- if _, ok = patterns[k]; ok {
+ if _, ok = patternsN[h]; ok {
hit = true
if deleteMatched && !invertMatch {
- delete(patterns, k)
+ delete(patternsN, h)
}
}
}
=====================================
seqkit/cmd/pair.go
=====================================
@@ -44,16 +44,15 @@ var pairCmd = &cobra.Command{
Short: "match up paired-end reads from two fastq files",
Long: `match up paired-end reads from two fastq files
-Attensions:
+Attentions:
1. Orders of headers in the two files better be the same (not shuffled),
- otherwise it consumes huge number of memory for buffering reads in memory.
+ otherwise, it consumes a huge number of memory for buffering reads in memory.
2. Unpaired reads are optional outputted with the flag -u/--save-unpaired.
-3. If the flag -O/--out-dir not given, output will be saved in the same directory
- of input, with suffix "paired", e.g., read_1.paired.fq.gz.
- Otherwise names are kept untouched in the given output directory.
+3. If the flag -O/--out-dir is not given, the output will be saved in the same directory
+ of input, with the suffix "paired", e.g., read_1.paired.fq.gz.
+ Otherwise, names are kept untouched in the given output directory.
4. Paired gzipped files may be slightly larger than original files, because
- of using different gzip package/library, don't worry.
-
+ of using a different gzip package/library, don't worry.
`,
Run: func(cmd *cobra.Command, args []string) {
config := getConfigs(cmd)
@@ -275,11 +274,6 @@ Attensions:
// left reads
if len(m1) > 0 && len(m2) > 0 {
for h1, r1 = range m1 {
-
- if string(r1.ID) == "A00582:209:HWWJCDSXX:1:1101:8314:2581" {
- fmt.Println("shit----")
- }
-
if r2, ok2 = m2[h1]; ok2 {
// output paired reads
r1.FormatToWriter(outfh1, lineWidth)
=====================================
seqkit/cmd/rename.go
=====================================
@@ -27,6 +27,7 @@ import (
"path/filepath"
"runtime"
+ "github.com/cespare/xxhash/v2"
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/bio/seqio/fastx"
"github.com/shenwei356/util/pathutil"
@@ -119,10 +120,9 @@ Example:
var record *fastx.Record
var fastxReader *fastx.Reader
var newID string
- var k string
+ var k uint64
var ok bool
- var numbers map[string]int
- numbers = make(map[string]int)
+ numbers := make(map[uint64]int, 1<<20)
for _, file := range files {
func(file string) {
fastxReader, err = fastx.NewReader(alphabet, file, idRegexp)
@@ -149,9 +149,9 @@ Example:
}
if byName {
- k = string(record.Name)
+ k = xxhash.Sum64(record.Name)
} else {
- k = string(record.ID)
+ k = xxhash.Sum64(record.ID)
}
if _, ok = numbers[k]; ok {
=====================================
seqkit/cmd/seq.go
=====================================
@@ -43,8 +43,8 @@ import (
// seqCmd represents the seq command
var seqCmd = &cobra.Command{
Use: "seq",
- Short: "transform sequences (extract ID, filter by length, remove gaps...)",
- Long: `transform sequences (extract ID, filter by length, remove gaps...)
+ Short: "transform sequences (extract ID, filter by length, remove gaps, reverse complement...)",
+ Long: `transform sequences (extract ID, filter by length, remove gaps, reverse complement...)
`,
Run: func(cmd *cobra.Command, args []string) {
=====================================
seqkit/cmd/split.go
=====================================
@@ -47,7 +47,7 @@ var splitCmd = &cobra.Command{
part size or number of parts.
If you just want to split by parts or sizes, please use "seqkit split2",
-which also apply for paired- and single-end FASTQ.
+which also applies for paired- and single-end FASTQ.
The definition of region is 1-based and with some custom design.
@@ -90,17 +90,35 @@ Examples:
outdir := getFlagString(cmd, "out-dir")
force := getFlagBool(cmd, "force")
+ extension := getFlagString(cmd, "extension")
+
+ prefixBySize := getFlagString(cmd, "by-size-prefix")
+ prefixByPart := getFlagString(cmd, "by-part-prefix")
+ prefixByID := getFlagString(cmd, "by-id-prefix")
+ prefixByRegion := getFlagString(cmd, "by-region-prefix")
+
+ prefixBySizeSet := cmd.Flags().Lookup("by-size-prefix").Changed
+ prefixByPartSet := cmd.Flags().Lookup("by-part-prefix").Changed
+ prefixByIDSet := cmd.Flags().Lookup("by-id-prefix").Changed
+ prefixByRegionSet := cmd.Flags().Lookup("by-region-prefix").Changed
+
file := files[0]
isstdin := isStdin(file)
- var fileName, fileExt string
+ var fileName, fileExt, fileExt2 string
if isstdin {
- fileName, fileExt = "stdin", ".fastx"
+ fileName, fileExt = "stdin", extension
if outdir == "" {
outdir = "stdin.split"
}
} else {
- fileName, fileExt = filepathTrimExtension(file)
+ fileName, fileExt, fileExt2 = filepathTrimExtension2(file, nil)
+ if extension != "" {
+ fileExt += extension
+ } else {
+ fileExt += fileExt2
+ }
+
if outdir == "" {
outdir = file + ".split"
}
@@ -108,6 +126,7 @@ Examples:
renameFileExt := true
var outfile string
+ var prefix string
var record *fastx.Record
var fastxReader *fastx.Reader
@@ -163,22 +182,33 @@ Examples:
if renameFileExt && isstdin {
if len(record.Seq.Qual) > 0 {
- fileExt = suffixFQ
+ fileExt = suffixFQ + extension
} else {
- fileExt = suffixFA
+ fileExt = suffixFA + extension
}
renameFileExt = false
}
records = append(records, record.Clone())
if len(records) == size {
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i, fileExt))
+ if prefixBySizeSet {
+ prefix = prefixBySize
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i, fileExt))
writeSeqs(records, outfile, config.LineWidth, quiet, dryRun)
i++
records = []*fastx.Record{}
}
}
if len(records) > 0 {
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i, fileExt))
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i, fileExt))
+ if prefixBySizeSet {
+ prefix = prefixBySize
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i, fileExt))
writeSeqs(records, outfile, config.LineWidth, quiet, dryRun)
}
@@ -212,9 +242,9 @@ Examples:
checkError(err)
if renameFileExt && isstdin {
if isFastq {
- fileExt = suffixFQ
+ fileExt = suffixFQ + extension
} else {
- fileExt = suffixFA
+ fileExt = suffixFA + extension
}
renameFileExt = false
}
@@ -244,7 +274,13 @@ Examples:
n := 1
if len(IDs) > 0 {
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), n, fileExt))
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), n, fileExt))
+ if prefixBySizeSet {
+ prefix = prefixBySize
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, n, fileExt))
if !dryRun {
outfh, err = xopen.Wopen(outfile)
checkError(err)
@@ -271,7 +307,13 @@ Examples:
log.Infof("write %d sequences to file: %s\n", j, outfile)
}
n++
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), n, fileExt))
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), n, fileExt))
+ if prefixBySizeSet {
+ prefix = prefixBySize
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, n, fileExt))
if !dryRun {
outfh.Close()
outfh, err = xopen.Wopen(outfile)
@@ -283,6 +325,9 @@ Examples:
if j > 0 && !quiet {
log.Infof("write %d sequences to file: %s\n", j, outfile)
}
+ if j == 0 {
+ os.Remove(outfile)
+ }
if !dryRun {
outfh.Close()
}
@@ -330,22 +375,34 @@ Examples:
for _, record := range allRecords {
if renameFileExt && isstdin {
if len(record.Seq.Qual) > 0 {
- fileExt = suffixFQ
+ fileExt = suffixFQ + extension
} else {
- fileExt = suffixFA
+ fileExt = suffixFA + extension
}
renameFileExt = false
}
records = append(records, record)
if len(records) == size {
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i, fileExt))
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i, fileExt))
+ if prefixByPartSet {
+ prefix = prefixByPart
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i, fileExt))
writeSeqs(records, outfile, config.LineWidth, quiet, dryRun)
i++
records = []*fastx.Record{}
}
}
if len(records) > 0 {
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i, fileExt))
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i, fileExt))
+ if prefixByPartSet {
+ prefix = prefixByPart
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i, fileExt))
writeSeqs(records, outfile, config.LineWidth, quiet, dryRun)
}
return
@@ -378,9 +435,9 @@ Examples:
checkError(err)
if renameFileExt && isstdin {
if isFastq {
- fileExt = suffixFQ
+ fileExt = suffixFQ + extension
} else {
- fileExt = suffixFA
+ fileExt = suffixFA + extension
}
renameFileExt = false
}
@@ -422,7 +479,13 @@ Examples:
n := 1
if len(IDs) > 0 {
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), n, fileExt))
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), n, fileExt))
+ if prefixByPartSet {
+ prefix = prefixByPart
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, n, fileExt))
if !dryRun {
outfh, err = xopen.Wopen(outfile)
checkError(err)
@@ -449,7 +512,13 @@ Examples:
log.Infof("write %d sequences to file: %s\n", j, outfile)
}
n++
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), n, fileExt))
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), n, fileExt))
+ if prefixByPartSet {
+ prefix = prefixByPart
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, n, fileExt))
if !dryRun {
outfh.Close()
outfh, err = xopen.Wopen(outfile)
@@ -503,9 +572,9 @@ Examples:
for _, record := range allRecords {
if renameFileExt && isstdin {
if len(record.Seq.Qual) > 0 {
- fileExt = suffixFQ
+ fileExt = suffixFQ + extension
} else {
- fileExt = suffixFA
+ fileExt = suffixFA + extension
}
renameFileExt = false
}
@@ -518,8 +587,16 @@ Examples:
var outfile string
for id, records := range recordsByID {
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.id_%s%s",
- filepath.Base(fileName),
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.id_%s%s",
+ // filepath.Base(fileName),
+ // pathutil.RemoveInvalidPathChars(id, "__"), fileExt))
+ if prefixByIDSet {
+ prefix = prefixByID
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%s%s",
+ prefix,
pathutil.RemoveInvalidPathChars(id, "__"), fileExt))
writeSeqs(records, outfile, config.LineWidth, quiet, dryRun)
}
@@ -553,9 +630,9 @@ Examples:
checkError(err)
if renameFileExt && isstdin {
if isFastq {
- fileExt = suffixFQ
+ fileExt = suffixFQ + extension
} else {
- fileExt = suffixFA
+ fileExt = suffixFA + extension
}
renameFileExt = false
}
@@ -612,8 +689,16 @@ Examples:
}()
var outfh *xopen.Writer
var err error
- outfile := filepath.Join(outdir, fmt.Sprintf("%s.id_%s%s",
- filepath.Base(fileName),
+ // outfile := filepath.Join(outdir, fmt.Sprintf("%s.id_%s%s",
+ // filepath.Base(fileName),
+ // pathutil.RemoveInvalidPathChars(id, "__"), fileExt))
+ if prefixByIDSet {
+ prefix = prefixByID
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%s%s",
+ prefix,
pathutil.RemoveInvalidPathChars(id, "__"), fileExt))
if !dryRun {
@@ -692,9 +777,9 @@ Examples:
for _, record := range allRecords {
if renameFileExt && isstdin {
if len(record.Seq.Qual) > 0 {
- fileExt = suffixFQ
+ fileExt = suffixFQ + extension
} else {
- fileExt = suffixFA
+ fileExt = suffixFA + extension
}
renameFileExt = false
}
@@ -711,7 +796,13 @@ Examples:
var outfile string
for subseq, records := range recordsBySeqs {
- outfile = filepath.Join(outdir, fmt.Sprintf("%s.region_%d:%d_%s%s", filepath.Base(fileName), start, end, subseq, fileExt))
+ // outfile = filepath.Join(outdir, fmt.Sprintf("%s.region_%d:%d_%s%s", filepath.Base(fileName), start, end, subseq, fileExt))
+ if prefixByRegionSet {
+ prefix = prefixByRegion
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%d:%d_%s%s", prefix, start, end, subseq, fileExt))
writeSeqs(records, outfile, config.LineWidth, quiet, dryRun)
}
return
@@ -743,16 +834,16 @@ Examples:
alphabet2, isFastq, err = fastx.GuessAlphabet(newFile)
if renameFileExt && isstdin {
if isFastq {
- fileExt = suffixFQ
+ fileExt = suffixFQ + extension
} else {
- fileExt = suffixFA
+ fileExt = suffixFA + extension
}
renameFileExt = false
}
checkError(err)
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
@@ -814,7 +905,13 @@ Examples:
var outfh *xopen.Writer
var err error
- outfile := filepath.Join(outdir, fmt.Sprintf("%s.region_%d:%d_%s%s", filepath.Base(fileName), start, end, subseq, fileExt))
+ // outfile := filepath.Join(outdir, fmt.Sprintf("%s.region_%d:%d_%s%s", filepath.Base(fileName), start, end, subseq, fileExt))
+ if prefixByRegionSet {
+ prefix = prefixByRegion
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile = filepath.Join(outdir, fmt.Sprintf("%s%d:%d_%s%s", prefix, start, end, subseq, fileExt))
if !dryRun {
outfh, err = xopen.Wopen(outfile)
@@ -863,6 +960,13 @@ func init() {
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")
+
+ splitCmd.Flags().StringP("by-size-prefix", "", "", "file prefix for --by-size")
+ splitCmd.Flags().StringP("by-part-prefix", "", "", "file prefix for --by-part")
+ splitCmd.Flags().StringP("by-id-prefix", "", "", "file prefix for --by-id")
+ splitCmd.Flags().StringP("by-region-prefix", "", "", "file prefix for --by-region")
+
+ splitCmd.Flags().StringP("extension", "e", "", `set output file extension, e.g., ".gz", ".xz", or ".zst"`)
}
var suffixFA = ".fasta"
=====================================
seqkit/cmd/split2.go
=====================================
@@ -49,8 +49,7 @@ occupation and fast speed.
The prefix of output files:
1. For stdin: stdin
2. Others: same to the input file
- 3. Set via the option: -o/--out-file, e.g., outputting xxx.part_001.fasta:
- cat ../tests/hairpin.fa | ./seqkit split2 -p 2 -O test -o xxx
+ 3. Set via the options: --by-length-prefix, --by-part-prefix, or --by-size-prefix
The extension of output files:
1. For stdin: .fast[aq]
@@ -99,8 +98,17 @@ The extension of output files:
outdir := getFlagString(cmd, "out-dir")
force := getFlagBool(cmd, "force")
+
extension := getFlagString(cmd, "extension")
+ prefixBySize := getFlagString(cmd, "by-size-prefix")
+ prefixByPart := getFlagString(cmd, "by-part-prefix")
+ prefixByLength := getFlagString(cmd, "by-length-prefix")
+
+ prefixBySizeSet := cmd.Flags().Lookup("by-size-prefix").Changed
+ prefixByPartSet := cmd.Flags().Lookup("by-part-prefix").Changed
+ prefixByLengthSet := cmd.Flags().Lookup("by-length-prefix").Changed
+
if size == 0 && parts == 0 && length == 0 {
checkError(fmt.Errorf(`one of flags should be given: -s/-p/-l. type "seqkit split2 -h" for help`))
}
@@ -218,12 +226,14 @@ The extension of output files:
var counts []int
var outfiles []string
+ // by size or by length
+ var outfhPre *xopen.Writer
+ var prefix string
+ var outfilePre string
+
var flag bool
if bySize || byLength { // by size or by length
- outfhs = make([]*xopen.Writer, 0, 10)
- counts = make([]int, 0, 10)
- outfiles = make([]string, 0, 10)
} else if byParts { // by part
outfhs = make([]*xopen.Writer, 0, parts)
counts = make([]int, 0, parts)
@@ -237,6 +247,7 @@ The extension of output files:
i := 0 // nth part
j := 0
var n int64 // length sum
+ once := true
for {
record, err = fastxReader.Read()
if err != nil {
@@ -247,141 +258,170 @@ The extension of output files:
break
}
- if fastxReader.IsFastq {
- config.LineWidth = 0
- fastx.ForcelyOutputFastq = true
- }
+ if once {
+ if fastxReader.IsFastq {
+ config.LineWidth = 0
+ fastx.ForcelyOutputFastq = true
+ }
- if renameFileExt && isstdin {
- if len(record.Seq.Qual) > 0 {
- fileExt = suffixFQ + extension
- } else {
- fileExt = suffixFA + extension
+ if renameFileExt && isstdin {
+ if len(record.Seq.Qual) > 0 {
+ fileExt = suffixFQ + extension
+ } else {
+ fileExt = suffixFA + extension
+ }
+ renameFileExt = false
}
- renameFileExt = false
+ once = false
}
+
n += int64(len(record.Seq.Seq))
if bySize {
if j == size {
- outfhs[i].Close()
+ outfhPre.Close()
if !quiet {
- log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+ log.Infof("write %d sequences to file: %s\n", j, outfilePre)
}
- outfhs[i] = nil
i++
+
+ if prefixBySizeSet {
+ prefix = prefixBySize
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfilePre = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i+1, fileExt))
+ outfhPre, err = xopen.Wopen(outfilePre)
+ checkError(err)
+
+ j = 0
+ }
+ } else if byLength {
+ flag = false
+
+ if outfhPre == nil { // first record
var outfh2 *xopen.Writer
- outfile := filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i+1, fileExt))
+ if prefixByLengthSet {
+ prefix = prefixByLength
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile := filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i+1, fileExt))
outfh2, err = xopen.Wopen(outfile)
checkError(err)
- outfhs = append(outfhs, outfh2)
- counts = append(counts, 0)
- outfiles = append(outfiles, outfile)
+ outfhPre = outfh2
+ outfilePre = outfile
j = 0
}
- } else if byLength {
- flag = false
+
if n >= length {
- if len(outfhs) == 0 { // order is different
- var outfh2 *xopen.Writer
- outfile := filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i+1, fileExt))
- outfh2, err = xopen.Wopen(outfile)
- checkError(err)
-
- outfhs = append(outfhs, outfh2)
- counts = append(counts, 0)
- outfiles = append(outfiles, outfile)
-
- record.FormatToWriter(outfhs[i], config.LineWidth)
- counts[i]++
-
- outfhs[i].Close()
- if !quiet {
- log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
- }
- outfhs[i] = nil
- i++
-
- n = 0
+ record.FormatToWriter(outfhPre, config.LineWidth)
+ j++
+
+ outfhPre.Close()
+ if !quiet {
+ log.Infof("write %d sequences to file: %s\n", j, outfilePre)
+ }
+ i++
+
+ var outfh2 *xopen.Writer
+
+ if prefixByLengthSet {
+ prefix = prefixByLength
} else {
- record.FormatToWriter(outfhs[i], config.LineWidth)
- counts[i]++
-
- outfhs[i].Close()
- if !quiet {
- log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
- }
- outfhs[i] = nil
- i++
-
- var outfh2 *xopen.Writer
- outfile := filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i+1, fileExt))
- outfh2, err = xopen.Wopen(outfile)
- checkError(err)
-
- outfhs = append(outfhs, outfh2)
- counts = append(counts, 0)
- outfiles = append(outfiles, outfile)
-
- n = 0
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
}
+ outfile := filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i+1, fileExt))
+ outfh2, err = xopen.Wopen(outfile)
+ checkError(err)
+
+ outfhPre = outfh2
+ outfilePre = outfile
+
+ j = 0
+ n = 0
flag = false
} else { // write this record later
flag = true
}
}
- if i+1 > len(outfhs) || outfhs[i] == nil {
- var outfh2 *xopen.Writer
- outfile := filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i+1, fileExt))
- outfh2, err = xopen.Wopen(outfile)
- checkError(err)
+ if bySize {
+ // first record, for bySize
+ if outfhPre == nil {
+ if prefixBySizeSet {
+ prefix = prefixBySize
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfilePre = filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i+1, fileExt))
+ outfhPre, err = xopen.Wopen(outfilePre)
+ checkError(err)
- outfhs = append(outfhs, outfh2)
- counts = append(counts, 0)
- outfiles = append(outfiles, outfile)
- }
+ j = 0
+ }
- if byLength {
+ record.FormatToWriter(outfhPre, config.LineWidth)
+
+ j++ // increase size
+ } else if byLength {
if flag {
- record.FormatToWriter(outfhs[i], config.LineWidth)
- counts[i]++
+ record.FormatToWriter(outfhPre, config.LineWidth)
+
+ j++
}
} else {
+ // first record, for byParts
+ if i+1 > len(outfhs) {
+ var outfh2 *xopen.Writer
+ if prefixByPartSet {
+ prefix = prefixByPart
+ } else {
+ prefix = fmt.Sprintf("%s.part_", filepath.Base(fileName))
+ }
+ outfile := filepath.Join(outdir, fmt.Sprintf("%s%03d%s", prefix, i+1, fileExt))
+ outfh2, err = xopen.Wopen(outfile)
+ checkError(err)
+
+ outfhs = append(outfhs, outfh2)
+ counts = append(counts, 0)
+ outfiles = append(outfiles, outfile)
+ }
+
record.FormatToWriter(outfhs[i], config.LineWidth)
counts[i]++
- }
- if bySize {
- j++ // increase size
- } else if byParts {
i++
if i == parts { // reset index
i = 0
}
- } else {
-
}
+
}
- // for by-size: only log last part,
- // for by-parts: log all parts.
- for i, outfh := range outfhs {
- if outfh == nil {
- continue
- }
- outfh.Close()
+ if byParts {
+ for i, outfh := range outfhs {
+ outfh.Close()
- if !quiet {
- if counts[i] == 0 {
- os.Remove(outfiles[i])
- } else {
- log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+ if !quiet {
+ if counts[i] == 0 {
+
+ } else {
+ log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+ }
}
}
+ } else {
+ outfhPre.Close()
+
+ if j == 0 {
+ os.Remove(outfilePre)
+ } else {
+ log.Infof("write %d sequences to file: %s\n", j, outfilePre)
+ }
}
}(file)
@@ -402,5 +442,9 @@ func init() {
split2Cmd.Flags().StringP("out-dir", "O", "", "output directory (default value is $infile.split)")
split2Cmd.Flags().BoolP("force", "f", false, "overwrite output directory")
+ split2Cmd.Flags().StringP("by-size-prefix", "", "", "file prefix for --by-size")
+ split2Cmd.Flags().StringP("by-part-prefix", "", "", "file prefix for --by-part")
+ split2Cmd.Flags().StringP("by-length-prefix", "", "", "file prefix for --by-length")
+
split2Cmd.Flags().StringP("extension", "e", "", `set output file extension, e.g., ".gz", ".xz", or ".zst"`)
}
=====================================
seqkit/cmd/stat.go
=====================================
@@ -72,6 +72,7 @@ Tips:
}
}
gapLettersBytes := []byte(gapLetters)
+ gcLettersBytes := []byte{'g', 'c', 'G', 'C'}
all := getFlagBool(cmd, "all")
tabular := getFlagBool(cmd, "tabular")
@@ -100,7 +101,7 @@ Tips:
"max_len",
}
if all {
- colnames = append(colnames, []string{"Q1", "Q2", "Q3", "sum_gap", "N50", "Q20(%)", "Q30(%)"}...)
+ colnames = append(colnames, []string{"Q1", "Q2", "Q3", "sum_gap", "N50", "Q20(%)", "Q30(%)", "GC(%)"}...)
}
outfh.WriteString(strings.Join(colnames, "\t") + "\n")
}
@@ -142,7 +143,7 @@ Tips:
info.lenAvg,
info.lenMax))
} else {
- outfh.WriteString(fmt.Sprintf("%s\t%s\t%s\t%d\t%d\t%d\t%.1f\t%d\t%.1f\t%.1f\t%.1f\t%d\t%d\t%.2f\t%.2f\n",
+ outfh.WriteString(fmt.Sprintf("%s\t%s\t%s\t%d\t%d\t%d\t%.1f\t%d\t%.1f\t%.1f\t%.1f\t%d\t%d\t%.2f\t%.2f\t%.2f\n",
info.file,
info.format,
info.t,
@@ -157,7 +158,8 @@ Tips:
info.gapSum,
info.N50,
info.q20,
- info.q30))
+ info.q30,
+ info.gc))
}
}
id++
@@ -178,7 +180,7 @@ Tips:
info1.lenAvg,
info1.lenMax))
} else {
- outfh.WriteString(fmt.Sprintf("%s\t%s\t%s\t%d\t%d\t%d\t%.1f\t%d\t%.1f\t%.1f\t%.1f\t%d\t%d\t%.2f\t%.2f\n",
+ outfh.WriteString(fmt.Sprintf("%s\t%s\t%s\t%d\t%d\t%d\t%.1f\t%d\t%.1f\t%.1f\t%.1f\t%d\t%d\t%.2f\t%.2f\t%.2f\n",
info1.file,
info1.format,
info1.t,
@@ -193,7 +195,8 @@ Tips:
info1.gapSum,
info1.N50,
info1.q20,
- info1.q30))
+ info1.q30,
+ info1.gc))
}
}
@@ -231,7 +234,7 @@ Tips:
info.lenAvg,
info.lenMax))
} else {
- outfh.WriteString(fmt.Sprintf("%s\t%s\t%s\t%d\t%d\t%d\t%.1f\t%d\t%.1f\t%.1f\t%.1f\t%d\t%d\t%.2f\t%.2f\n",
+ outfh.WriteString(fmt.Sprintf("%s\t%s\t%s\t%d\t%d\t%d\t%.1f\t%d\t%.1f\t%.1f\t%.1f\t%d\t%d\t%.2f\t%.2f\t%.2f\n",
info.file,
info.format,
info.t,
@@ -246,7 +249,8 @@ Tips:
info.gapSum,
info.N50,
info.q20,
- info.q30))
+ info.q30,
+ info.gc))
}
}
}
@@ -290,6 +294,7 @@ Tips:
}()
var gapSum uint64
+ var gcSum uint64
lensStats := util.NewLengthStats()
@@ -361,6 +366,7 @@ Tips:
}
gapSum += uint64(byteutil.CountBytes(record.Seq.Seq, gapLettersBytes))
+ gcSum += uint64(byteutil.CountBytes(record.Seq.Seq, gcLettersBytes))
}
}
@@ -399,7 +405,7 @@ Tips:
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0,
- 0, 0,
+ 0, 0, 0,
nil, id}
} else {
if basename {
@@ -413,6 +419,7 @@ Tips:
math.Round(lensStats.Mean(), 1), lensStats.Max(), n50, l50,
q1, q2, q3,
math.Round(float64(q20)/float64(lensStats.Sum())*100, 2), math.Round(float64(q30)/float64(lensStats.Sum())*100, 2),
+ math.Round(float64(gcSum)/float64(lensStats.Sum())*100, 2),
nil, id}
}
}(file, id)
@@ -453,6 +460,7 @@ Tips:
{Header: "N50", AlignRight: true},
{Header: "Q20(%)", AlignRight: true},
{Header: "Q30(%)", AlignRight: true},
+ {Header: "GC(%)", AlignRight: true},
// {Header: "L50", AlignRight: true},
}...)
}
@@ -490,6 +498,7 @@ Tips:
humanize.Comma(int64(info.N50)),
humanize.Commaf(info.q20),
humanize.Commaf(info.q30),
+ humanize.Commaf(info.gc),
// humanize.Comma(info.L50),
)
}
@@ -520,6 +529,8 @@ type statInfo struct {
q20 float64
q30 float64
+ gc float64
+
err error
id uint64
}
=====================================
seqkit/cmd/version.go
=====================================
@@ -29,7 +29,7 @@ import (
)
// VERSION of seqkit
-const VERSION = "2.2.0"
+const VERSION = "2.3.0"
// versionCmd represents the version command
var versionCmd = &cobra.Command{
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/39e24c11adffc9a3e0c472fdf01b69ddd7212d4b...50f12697d668718e807b3af3117be2773ca98aa9
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/39e24c11adffc9a3e0c472fdf01b69ddd7212d4b...50f12697d668718e807b3af3117be2773ca98aa9
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