[med-svn] [Git][med-team/seqkit][master] 6 commits: New upstream version 0.15.0+ds
Nilesh Patra
gitlab at salsa.debian.org
Thu Jan 14 11:24:55 GMT 2021
Nilesh Patra pushed to branch master at Debian Med / seqkit
Commits:
8fdd687f by Nilesh Patra at 2021-01-14T16:34:12+05:30
New upstream version 0.15.0+ds
- - - - -
9b11be4f by Nilesh Patra at 2021-01-14T16:34:53+05:30
Update upstream source from tag 'upstream/0.15.0+ds'
Update to upstream version '0.15.0+ds'
with Debian dir 44933e56f95acf3b4de739db5edd9f76c7c372c8
- - - - -
be31dbb8 by Nilesh Patra at 2021-01-14T16:45:19+05:30
Refresh patch
- - - - -
e8c2e976 by Nilesh Patra at 2021-01-14T11:17:17+00:00
Update manpage
- - - - -
f5cc172e by Nilesh Patra at 2021-01-14T11:17:44+00:00
Declare compliance with policy 4.5.1
- - - - -
6d382365 by Nilesh Patra at 2021-01-14T16:48:36+05:30
Update changelog
- - - - -
20 changed files:
- CHANGES.md
- debian/changelog
- debian/control
- debian/patches/spellings.patch
- debian/seqkit-benchmark.1
- debian/seqkit.1
- doc/docs/download.md
- doc/docs/usage.md
- + go.mod
- + go.sum
- seqkit/cmd/amplicon.go
- seqkit/cmd/bam_toolbox.go
- seqkit/cmd/grep.go
- seqkit/cmd/locate.go
- seqkit/cmd/seq.go
- seqkit/cmd/shuffle.go
- seqkit/cmd/split2.go
- seqkit/cmd/version.go
- seqkit/packaging.sh
- tests/test.sh
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,3 +1,11 @@
+- [SeqKit v0.15.0](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
+[](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
+ - `seqkit grep/locate`: update help message.
+ - `seqkit grep`: **search on both strand when searching by sequence**.
+ - `seqkit split2`: fix redundant log when using `-s`.
+ - `seqkit bam`: new field `RightSoftClipSeq`. [#172](https://github.com/shenwei356/seqkit/pull/172)
+ - `seqkit sample -2`: remove extra `\n`. [#173](https://github.com/shenwei356/seqkit/issues/173)
+ - `seqkit split2 -l`: fix bug for splitting by accumulative length, this bug occurs when the first record is longer than `-l`, no sequences are lost.
- [SeqKit v0.14.0](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
[](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
- new command `seqkit pair`: match up paired-end reads from two fastq files, faster than fastq-pair.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+seqkit (0.15.0+ds-1) unstable; urgency=medium
+
+ * New upstream version 0.15.0+ds
+ * Refresh patch
+ * Update manpage
+ * Declare compliance with policy 4.5.1
+
+ -- Nilesh Patra <npatra974 at gmail.com> Thu, 14 Jan 2021 11:17:52 +0000
+
seqkit (0.14.0+ds-1) unstable; urgency=medium
* New upstream version 0.14.0+ds
=====================================
debian/control
=====================================
@@ -25,7 +25,7 @@ Build-Depends: debhelper-compat (= 13),
golang-github-iafan-cwalk-dev,
golang-github-smallfish-simpleyaml-dev,
samtools
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/seqkit
Vcs-Git: https://salsa.debian.org/med-team/seqkit.git
Homepage: https://github.com/shenwei356/seqkit
=====================================
debian/patches/spellings.patch
=====================================
@@ -38,7 +38,7 @@ Last Changed: August 3, 2020
Attentions:
- 1. Mutiple point mutations (-p/--point) are allowed, but only single
-+ 1. Multiple 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.
@@ -84,7 +84,7 @@ Last Changed: August 3, 2020
}
var nseqs int
-@@ -231,5 +231,5 @@
+@@ -230,5 +230,5 @@
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)")
@@ -173,10 +173,10 @@ Last Changed: August 3, 2020
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.
-
- Examples:
- 0. no region given.
++ 2. Mismatch is allowed, but the mismatch location (5' or 3') is not controlled.
+ 3. Degenerate bases/residues like "RYMM.." are also supported.
+ But do not use degenerate bases/residues in regular expression, you need
+ convert them to regular expression, e.g., change "N" or "X" to ".".
--- a/seqkit/cmd/scat.go
+++ b/seqkit/cmd/scat.go
@@ -566,7 +566,7 @@
@@ -188,3 +188,14 @@ Last Changed: August 3, 2020
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")
+--- a/seqkit/cmd/pair.go
++++ b/seqkit/cmd/pair.go
+@@ -65,7 +65,7 @@
+ 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")
=====================================
debian/seqkit-benchmark.1
=====================================
@@ -1,5 +1,5 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
-.TH SEQKIT-BENCHMARK "1" "October 2020" "seqkit-benchmark 0.14.0+ds" "User Commands"
+.TH SEQKIT-BENCHMARK "1" "January 2021" "seqkit-benchmark 0.15.0+ds" "User Commands"
.SH NAME
seqkit-benchmark \- cross-platform and ultrafast toolkit for FASTA/Q file manipulation
.SH DESCRIPTION
=====================================
debian/seqkit.1
=====================================
@@ -1,11 +1,11 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
-.TH SEQKIT "1" "October 2020" "seqkit 0.14.0+ds" "User Commands"
+.TH SEQKIT "1" "January 2021" "seqkit 0.15.0+ds" "User Commands"
.SH NAME
seqkit \- cross-platform and ultrafast toolkit for FASTA/Q file manipulation
.SH DESCRIPTION
SeqKit \fB\-\-\fR a cross\-platform and ultrafast toolkit for FASTA/Q file manipulation
.PP
-Version: 0.14.0
+Version: 0.15.0
.PP
Author: Wei Shen <shenwei356 at gmail.com>
.PP
=====================================
doc/docs/download.md
=====================================
@@ -6,17 +6,14 @@ SeqKit is implemented in [Go](https://golang.org/) programming language,
## Latest Version
-- [SeqKit v0.14.0](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
-[](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
- - new command `seqkit pair`: match up paired-end reads from two fastq files, faster than fastq-pair.
- - `seqkit translate`: new flag `-F/--append-fram` for optional adding frame info to ID. [#159](https://github.com/shenwei356/seqkit/issues/159)
- - `seqkit stats`: reduce memory usage when using `-a` for calculating N50. [#153](https://github.com/shenwei356/seqkit/issues/153)
- - `seqkit mutate`: fix inserting sequence `-i/--insertion`,
- this bug occurs when `insert site` is big in some cases, don't worry if no error reported.
- - `seqkit replace`:
- - new flag `-U/--keep-untouched`: do not change anything when no value found for the key (only for sequence name).
- - do no support editing FASTQ sequence.
- - `seqkit grep/locate`: new flag `--circular` for supporting circular genome. [#158](https://github.com/shenwei356/seqkit/issues/158)
+- [SeqKit v0.15.0](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
+[](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
+ - `seqkit grep/locate`: update help message.
+ - `seqkit grep`: **search on both strand when searching by sequence**.
+ - `seqkit split2`: fix redundant log when using `-s`.
+ - `seqkit bam`: new field `RightSoftClipSeq`. [#172](https://github.com/shenwei356/seqkit/pull/172)
+ - `seqkit sample -2`: remove extra `\n`. [#173](https://github.com/shenwei356/seqkit/issues/173)
+ - `seqkit split2 -l`: fix bug for splitting by accumulative length, this bug occurs when the first record is longer than `-l`, no sequences are lost.
### Please cite
@@ -33,12 +30,13 @@ SeqKit is implemented in [Go](https://golang.org/) programming language,
OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/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/v0.14.0/seqkit_linux_386.tar.gz)
-Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/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/v0.14.0/seqkit_linux_amd64.tar.gz)
-OS X |32-bit |[seqkit_darwin_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_darwin_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_386.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_darwin_386.tar.gz)
-OS X |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/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/v0.14.0/seqkit_darwin_amd64.tar.gz)
-Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/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/v0.14.0/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/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/v0.14.0/seqkit_windows_amd64.exe.tar.gz)
+Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/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/v0.15.0/seqkit_linux_386.tar.gz)
+Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/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/v0.15.0/seqkit_linux_amd64.tar.gz)
+Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/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/v0.15.0/seqkit_linux_arm64.tar.gz)
+macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/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/v0.15.0/seqkit_darwin_amd64.tar.gz)
+macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/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/v0.15.0/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/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/v0.15.0/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/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/v0.15.0/seqkit_windows_amd64.exe.tar.gz)
## Installation
@@ -108,6 +106,17 @@ Howto:
## Release History
+- [SeqKit v0.14.0](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
+[](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
+ - new command `seqkit pair`: match up paired-end reads from two fastq files, faster than fastq-pair.
+ - `seqkit translate`: new flag `-F/--append-fram` for optional adding frame info to ID. [#159](https://github.com/shenwei356/seqkit/issues/159)
+ - `seqkit stats`: reduce memory usage when using `-a` for calculating N50. [#153](https://github.com/shenwei356/seqkit/issues/153)
+ - `seqkit mutate`: fix inserting sequence `-i/--insertion`,
+ this bug occurs when `insert site` is big in some cases, don't worry if no error reported.
+ - `seqkit replace`:
+ - new flag `-U/--keep-untouched`: do not change anything when no value found for the key (only for sequence name).
+ - do no support editing FASTQ sequence.
+ - `seqkit grep/locate`: new flag `--circular` for supporting circular genome. [#158](https://github.com/shenwei356/seqkit/issues/158)
- [SeqKit v0.13.2](https://github.com/shenwei356/seqkit/releases/tag/v0.13.2)
[](https://github.com/shenwei356/seqkit/releases/tag/v0.13.2)
- `seqkit sana`: fix bug causing hanging on empty files. [#149](https://github.com/shenwei356/seqkit/pull/149)
=====================================
doc/docs/usage.md
=====================================
@@ -174,7 +174,7 @@ reproduced in different environments with same random seed.
``` text
SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
-Version: 0.14.0
+Version: 0.15.0
Author: Wei Shen <shenwei356 at gmail.com>
@@ -283,6 +283,11 @@ Usage
``` text
transform sequences (revserse, complement, extract ID...)
+Attentions:
+
+ 1. This command outputs plain text even when out file ends with ".gz".
+
+
Usage:
seqkit seq [flags]
@@ -1372,12 +1377,20 @@ Attentions:
1. Unlike POSIX/GNU grep, we compare the pattern to the whole target
(ID/full header) by default. Please switch "-r/--use-regexp" on
for partly matching.
- 2. While when searching by sequences, only positive strand is searched,
- and it's partly matching.
+ 2. When searching by sequences, it's partly matching, and both positive
+ and negative strands are searched.
Mismatch is allowed using flag "-m/--max-mismatch",
but it's not fast enough for large genome like human genome.
Though, it's fast enough for microbial genomes.
- 3. The order of sequences in result is consistent with that in original
+ 3. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+ But do not use degenerate bases/residues in regular expression, you need
+ convert them to regular expression, e.g., change "N" or "X" to "."..
+ 4. When providing search patterns (motifs) via flag '-p',
+ please use double quotation marks for patterns containing comma,
+ e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+ parser accepts comma-separated-values (CSV) for multiple values (motifs).
+ Patterns in file do not follow this rule.
+ 5. The order of sequences in result is consistent with that in original
file, not the order of the query patterns.
But for FASTA file, you can use:
seqkit faidx seqs.fasta --infile-list IDs.txt
@@ -1404,26 +1417,27 @@ Usage:
seqkit grep [flags]
Flags:
- -n, --by-name match by full name instead of just ID
- -s, --by-seq search subseq on seq, only positive strand is searched, and mismatch allowed using flag -m/--max-mismatch
- -c --circular circular genome
- -d, --degenerate pattern/motif contains degenerate base
- --delete-matched delete a pattern right after being matched, this keeps the firstly matched data and speedups when using regular expressions
- -h, --help help for grep
- -i, --ignore-case ignore case
- -v, --invert-match invert the sense of matching, to select non-matching records
- -m, --max-mismatch int max mismatch when matching by seq. For large genomes like human genome, using mapping/alignment tools would be faster
- -p, --pattern strings search pattern (multiple values supported. Attention: use double quotation marks for patterns containing comma, e.g., -p '"A{2,}"'))
- -f, --pattern-file string pattern file (one record per line)
- -R, --region string specify sequence region for searching. e.g 1:12 for first 12 bases, -12:-1 for last 12 bases
- -r, --use-regexp patterns are regular expressio
+ -n, --by-name match by full name instead of just ID
+ -s, --by-seq search subseq on seq, both positive and negative strand are searched, and mismatch allowed using flag -m/--max-mismatch
+ -c, --circular circular genome
+ -d, --degenerate pattern/motif contains degenerate base
+ --delete-matched delete a pattern right after being matched, this keeps the firstly matched data and speedups when using regular expressions
+ -h, --help help for grep
+ -i, --ignore-case ignore case
+ -v, --invert-match invert the sense of matching, to select non-matching records
+ -m, --max-mismatch int max mismatch when matching by seq. For large genomes like human genome, using mapping/alignment tools would be faster
+ -P, --only-positive-strand only search on positive strand
+ -p, --pattern strings search pattern (multiple values supported. Attention: use double quotation marks for patterns containing comma, e.g., -p '"A{2,}"'))
+ -f, --pattern-file string pattern file (one record per line)
+ -R, --region string specify sequence region for searching. e.g 1:12 for first 12 bases, -12:-1 for last 12 bases
+ -r, --use-regexp patterns are regular expression
```
Examples
-1. Searching with list of sequence IDs (do not containing whitespace)
+1. Searching with list of sequence IDs (do not contain whitespace)
$ seqkit grep -f id.txt seqs.fq.gz -o result.fq.gz
@@ -1526,20 +1540,23 @@ Usage
``` text
locate subsequences/motifs, mismatch allowed
-Motifs could be EITHER plain sequence containing "ACTGN" OR regular
-expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
-Degenerate bases like "RYMM.." are also supported by flag -d.
-
-By default, motifs are treated as regular expression.
-When flag -d given, regular expression may be wrong.
-For example: "\w" will be wrongly converted to "\[AT]".
-
-Mismatch is allowed using flag "-m/--max-mismatch",
-but it's not fast enough for large genome like human genome.
-Though, it's fast enough for microbial genomes.
+Attentions:
-When using flag --circular, end position of matched subsequence that
-crossing genome sequence end would be greater than sequence length.
+ 1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
+ expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
+ 2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+ But do not use degenerate bases/residues in regular expression, you need
+ convert them to regular expression, e.g., change "N" or "X" to "."..
+ 3. When providing search patterns (motifs) via flag '-p',
+ please use double quotation marks for patterns containing comma,
+ e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+ parser accepts comma-separated-values (CSV) for multiple values (motifs).
+ Patterns in file do not follow this rule.
+ 4. Mismatch is allowed using flag "-m/--max-mismatch",
+ but it's not fast enough for large genome like human genome.
+ Though, it's fast enough for microbial genomes.
+ 5. When using flag --circular, end position of matched subsequence that
+ crossing genome sequence end would be greater than sequence length.
Usage:
seqkit locate [flags]
@@ -1760,6 +1777,9 @@ retrieve amplicon (or specific region around it) via primer(s).
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.
+ 3. Degenerate bases/residues like "RYMM.." are also supported.
+ But do not use degenerate bases/residues in regular expression, you need
+ convert them to regular expression, e.g., change "N" or "X" to "."..
Examples:
0. no region given.
@@ -1809,16 +1829,17 @@ Usage:
seqkit amplicon [flags]
Flags:
- --bed output in BED6+1 format with amplicon as 7th column
+ --bed output in BED6+1 format with amplicon as 7th columns
-f, --flanking-region region is flanking region
- -F, --forward string forward primer (5'-primer-3')
+ -F, --forward string forward primer (5'-primer-3'), degenerate bases allowed
-h, --help help for amplicon
- -m, --max-mismatch int max mismatch when matching primers
+ -m, --max-mismatch int max mismatch when matching primers, no degenerate bases allowed
-P, --only-positive-strand only search on positive strand
-p, --primer-file string 3- or 2-column tabular primer file, with first column as primer name
-r, --region string specify region to return. type "seqkit amplicon -h" for detail
- -R, --reverse string reverse primer (5'-primer-3')
+ -R, --reverse string reverse primer (5'-primer-3'), degenerate bases allowed
-s, --strict-mode strict mode, i.e., discarding seqs not fully matching (shorter) given region range
+
```
Examples
@@ -2181,7 +2202,7 @@ Usage:
seqkit split2 [flags]
Flags:
- -l, --by-length string split sequences into chunks of N bases, supports K/M/G suffix
+ -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
-f, --force overwrite output directory
=====================================
go.mod
=====================================
@@ -0,0 +1,36 @@
+module github.com/shenwei356/seqkit
+
+go 1.16
+
+require (
+ github.com/biogo/biogo v1.0.3
+ github.com/biogo/hts v1.2.2
+ github.com/bsipos/thist v1.0.0
+ github.com/cespare/xxhash v1.1.0
+ github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 // indirect
+ github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8
+ github.com/dustin/go-humanize v1.0.0
+ github.com/edsrzf/mmap-go v1.0.0 // indirect
+ github.com/fsnotify/fsnotify v1.4.9
+ github.com/iafan/cwalk v0.0.0-20191125092548-dd7f505d2f66
+ github.com/klauspost/compress v1.11.4 // indirect
+ github.com/klauspost/pgzip v1.2.5 // indirect
+ github.com/logrusorgru/aurora v2.0.3+incompatible
+ github.com/mattn/go-colorable v0.1.8
+ github.com/mattn/go-isatty v0.0.12
+ github.com/mattn/go-runewidth v0.0.9 // indirect
+ github.com/mitchellh/go-homedir v1.1.0
+ github.com/pkg/errors v0.9.1
+ github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
+ github.com/shenwei356/bio v0.0.0-20201213090627-18e3e643a476
+ github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 // indirect
+ github.com/shenwei356/breader v0.0.0-20170924140440-21f0a70fe179
+ github.com/shenwei356/bwt v0.0.0-20200418151221-ae79c9858c90
+ github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
+ github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d // indirect
+ github.com/shenwei356/util v0.0.0-20201214054755-2942125340cd
+ github.com/shenwei356/xopen v0.0.0-20181203091311-f4f16ddd3992
+ github.com/smallfish/simpleyaml v0.0.0-20170911015856-a32031077861
+ github.com/spf13/cobra v1.1.1
+ github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939
+)
=====================================
go.sum
=====================================
@@ -0,0 +1,386 @@
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+google.golang.org/genproto v0.0.0-20190801165951-fa694d86fc64/go.mod h1:DMBHOl98Agz4BDEuKkezgsaosCRResVns1a3J2ZsMNc=
+google.golang.org/genproto v0.0.0-20190819201941-24fa4b261c55/go.mod h1:DMBHOl98Agz4BDEuKkezgsaosCRResVns1a3J2ZsMNc=
+google.golang.org/genproto v0.0.0-20190911173649-1774047e7e51/go.mod h1:IbNlFCBrqXvoKpeg0TB2l7cyZUmoaFKYIwrEpbDKLA8=
+google.golang.org/genproto v0.0.0-20191108220845-16a3f7862a1a/go.mod h1:n3cpQtvxv34hfy77yVDNjmbRyujviMdxYliBSkLhpCc=
+google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c=
+google.golang.org/grpc v1.20.1/go.mod h1:10oTOabMzJvdu6/UiuZezV6QK5dSlG84ov/aaiqXj38=
+google.golang.org/grpc v1.21.1/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM=
+gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLkstjWtayDeSgw=
+gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo=
+gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI=
+gopkg.in/ini.v1 v1.51.0/go.mod h1:pNLf8WUiyNEtQjuu5G5vTm06TEv9tsIgeAvK8hOrP4k=
+gopkg.in/resty.v1 v1.12.0/go.mod h1:mDo4pnntr5jdWRML875a/NmxYqAlA73dVijT2AXvQQo=
+gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bli9HhUf9+ttbYbLASfIpnQbh74=
+gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+gopkg.in/yaml.v2 v2.2.8 h1:obN1ZagJSUGI0Ek/LBmuj4SNLPfIny3KsKFopxRdj10=
+gopkg.in/yaml.v2 v2.2.8/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.0-20190106161140-3f1c8253044a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.0-20190418001031-e561f6794a2a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.1-2019.2.3/go.mod h1:a3bituU0lyd329TUQxRnasdCoJDkEUEAqEt0JzvZhAg=
+rsc.io/binaryregexp v0.2.0/go.mod h1:qTv7/COck+e2FymRvadv62gMdZztPaShugOCi3I+8D8=
+rsc.io/pdf v0.1.1 h1:k1MczvYDUvJBe93bYd7wrZLLUEcLZAuF824/I4e5Xr4=
+rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4=
=====================================
seqkit/cmd/amplicon.go
=====================================
@@ -51,6 +51,9 @@ 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.
+ 3. Degenerate bases/residues like "RYMM.." are also supported.
+ But do not use degenerate bases/residues in regular expression, you need
+ convert them to regular expression, e.g., change "N" or "X" to "."..
Examples:
0. no region given.
@@ -135,7 +138,7 @@ Examples:
list, err = loadPrimers(primerFile)
checkError(err)
} else {
- list = [][3]string{[3]string{".", forward0, reverse0}}
+ list = [][3]string{{".", forward0, reverse0}}
}
primers, err = parsePrimers(list)
@@ -261,7 +264,7 @@ func init() {
ampliconCmd.Flags().StringP("forward", "F", "", "forward primer (5'-primer-3'), degenerate bases allowed")
ampliconCmd.Flags().StringP("reverse", "R", "", "reverse primer (5'-primer-3'), degenerate bases allowed")
- ampliconCmd.Flags().IntP("max-mismatch", "m", 0, "max mismatch when matching primers")
+ ampliconCmd.Flags().IntP("max-mismatch", "m", 0, "max mismatch when matching primers, no degenerate bases allowed")
ampliconCmd.Flags().StringP("primer-file", "p", "", "3- or 2-column tabular primer file, with first column as primer name")
ampliconCmd.Flags().StringP("region", "r", "", `specify region to return. type "seqkit amplicon -h" for detail`)
@@ -374,6 +377,9 @@ func NewAmpliconFinder(sequence, forwardPrimer, reversePrimerRC []byte, maxMisma
finder.FMindex = index
} else {
if seq.DNA.IsValid(finder.F) != nil { // containing degenerate base
+ if maxMismatch > 0 {
+ checkError(fmt.Errorf("it does not support both degenerate base and mismatch"))
+ }
s, _ := seq.NewSeq(seq.DNA, finder.F)
rF, err := regexp.Compile(s.Degenerate2Regexp())
if err != nil {
@@ -383,6 +389,9 @@ func NewAmpliconFinder(sequence, forwardPrimer, reversePrimerRC []byte, maxMisma
}
if seq.DNA.IsValid(finder.R) != nil { // containing degenerate base
+ if maxMismatch > 0 {
+ checkError(fmt.Errorf("it does not support both degenerate base and mismatch"))
+ }
s, _ := seq.NewSeq(seq.DNA, finder.R)
rR, err := regexp.Compile(s.Degenerate2Regexp())
if err != nil {
=====================================
seqkit/cmd/bam_toolbox.go
=====================================
@@ -457,7 +457,7 @@ func GetSamAlnDetails(r *sam.Record) *AlnDetails {
}
func BamToolDump(p *BamToolParams) {
- validFields := []string{"Read", "Ref", "Pos", "EndPos", "MapQual", "Acc", "Match", "Mismatch", "Ins", "Del", "AlnLen", "ReadLen", "RefLen", "RefAln", "RefCov", "ReadAln", "ReadCov", "Strand", "MeanQual", "LeftClip", "RightClip", "Flags", "IsSec", "IsSup", "ReadSeq", "ReadAlnSeq", "LeftSoftClipSeq", "RightSoftClip", "LeftHardClip", "RightHardClip"}
+ validFields := []string{"Read", "Ref", "Pos", "EndPos", "MapQual", "Acc", "Match", "Mismatch", "Ins", "Del", "AlnLen", "ReadLen", "RefLen", "RefAln", "RefCov", "ReadAln", "ReadCov", "Strand", "MeanQual", "LeftClip", "RightClip", "Flags", "IsSec", "IsSup", "ReadSeq", "ReadAlnSeq", "LeftSoftClipSeq", "RightSoftClipSeq", "RightSoftClip", "LeftHardClip", "RightHardClip"}
tsvFh := os.Stderr
tsvFile, err := p.Yaml.Get("Tsv").String()
=====================================
seqkit/cmd/grep.go
=====================================
@@ -46,17 +46,26 @@ var grepCmd = &cobra.Command{
Long: fmt.Sprintf(`search sequences by ID/name/sequence/sequence motifs, mismatch allowed
Attentions:
+
0. By default, we match sequence ID with patterns, use "-n/--by-name"
for matching full name instead of just ID.
1. Unlike POSIX/GNU grep, we compare the pattern to the whole target
(ID/full header) by default. Please switch "-r/--use-regexp" on
for partly matching.
- 2. While when searching by sequences, only positive strand is searched,
- and it's partly matching.
+ 2. When searching by sequences, it's partly matching, and both positive
+ and negative strands are searched.
Mismatch is allowed using flag "-m/--max-mismatch",
but it's not fast enough for large genome like human genome.
Though, it's fast enough for microbial genomes.
- 3. The order of sequences in result is consistent with that in original
+ 3. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+ But do not use degenerate bases/residues in regular expression, you need
+ convert them to regular expression, e.g., change "N" or "X" to "."..
+ 4. When providing search patterns (motifs) via flag '-p',
+ please use double quotation marks for patterns containing comma,
+ e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+ parser accepts comma-separated-values (CSV) for multiple values (motifs).
+ Patterns in file do not follow this rule.
+ 5. The order of sequences in result is consistent with that in original
file, not the order of the query patterns.
But for FASTA file, you can use:
seqkit faidx seqs.fasta --infile-list IDs.txt
@@ -88,6 +97,7 @@ Examples:
deleteMatched := getFlagBool(cmd, "delete-matched")
invertMatch := getFlagBool(cmd, "invert-match")
bySeq := getFlagBool(cmd, "by-seq")
+ onlyPositiveStrand := getFlagBool(cmd, "only-positive-strand")
mismatches := getFlagNonNegativeInt(cmd, "max-mismatch")
byName := getFlagBool(cmd, "by-name")
ignoreCase := getFlagBool(cmd, "ignore-case")
@@ -256,6 +266,7 @@ Examples:
checkError(err)
defer outfh.Close()
+ var sequence *seq.Seq
var target []byte
var ok, hit bool
var record *fastx.Record
@@ -264,6 +275,8 @@ Examples:
var locs []int
var re *regexp.Regexp
var p string
+ strands := []byte{'+', '-'}
+ var strand byte
for _, file := range files {
fastxReader, err = fastx.NewReader(alphabet, file, idRegexp)
checkError(err)
@@ -285,76 +298,101 @@ Examples:
if byName {
target = record.Name
} else if bySeq {
- if limitRegion {
- target = record.Seq.SubSeq(start, end).Seq
- } else if circular {
- // concat two copies of sequence, and do not change orginal sequence
- target = make([]byte, len(record.Seq.Seq)*2)
- copy(target[0:len(record.Seq.Seq)], record.Seq.Seq)
- copy(target[len(record.Seq.Seq):], record.Seq.Seq)
- } else {
- target = record.Seq.Seq
- }
+
} else {
target = record.ID
}
hit = false
- if degenerate || useRegexp {
- for p, re = range patterns {
- if re.Match(target) {
- hit = true
- if deleteMatched && !invertMatch {
- delete(patterns, p)
+ for _, strand = range strands {
+ if hit {
+ break
+ }
+
+ if strand == '-' {
+ if bySeq {
+ if onlyPositiveStrand {
+ break
}
+ } else {
break
}
}
- } else if bySeq {
- if ignoreCase {
- target = bytes.ToLower(target)
+
+ if bySeq {
+ sequence = record.Seq
+ if strand == '-' {
+ sequence = record.Seq.RevCom()
+ }
+ if limitRegion {
+ target = sequence.SubSeq(start, end).Seq
+ } else if circular {
+ // concat two copies of sequence, and do not change orginal sequence
+ target = make([]byte, len(sequence.Seq)*2)
+ copy(target[0:len(sequence.Seq)], sequence.Seq)
+ copy(target[len(sequence.Seq):], sequence.Seq)
+ } else {
+ target = sequence.Seq
+ }
}
- if mismatches == 0 {
- for k = range patterns {
- if bytes.Contains(target, []byte(k)) {
+
+ if degenerate || useRegexp {
+ for p, re = range patterns {
+ if re.Match(target) {
hit = true
if deleteMatched && !invertMatch {
- delete(patterns, k)
+ delete(patterns, p)
}
break
}
}
- } else {
- _, err = sfmi.Transform(target)
- if err != nil {
- checkError(fmt.Errorf("fail to build FMIndex for sequence: %s", record.Name))
+ } else if bySeq {
+ if ignoreCase {
+ target = bytes.ToLower(target)
}
- for k = range patterns {
- locs, err = sfmi.Locate([]byte(k), mismatches)
+ if mismatches == 0 {
+ for k = range patterns {
+ if bytes.Contains(target, []byte(k)) {
+ hit = true
+ if deleteMatched && !invertMatch {
+ delete(patterns, k)
+ }
+ break
+ }
+ }
+ } else {
+ _, err = sfmi.Transform(target)
if err != nil {
- checkError(fmt.Errorf("fail to search pattern '%s' on seq '%s': %s", k, record.Name, err))
+ checkError(fmt.Errorf("fail to build FMIndex for sequence: %s", record.Name))
}
- if len(locs) > 0 {
- hit = true
- if deleteMatched && !invertMatch {
- delete(patterns, k)
+ for k = range patterns {
+ locs, err = sfmi.Locate([]byte(k), mismatches)
+ if err != nil {
+ checkError(fmt.Errorf("fail to search pattern '%s' on seq '%s': %s", k, record.Name, err))
+ }
+ if len(locs) > 0 {
+ hit = true
+ if deleteMatched && !invertMatch {
+ delete(patterns, k)
+ }
+ break
}
- break
}
}
- }
- } else {
- k = string(target)
- if ignoreCase {
- k = strings.ToLower(k)
- }
- if _, ok = patterns[k]; ok {
- hit = true
- if deleteMatched && !invertMatch {
- delete(patterns, k)
+ } else {
+ k = string(target)
+ if ignoreCase {
+ k = strings.ToLower(k)
+ }
+ if _, ok = patterns[k]; ok {
+ hit = true
+ if deleteMatched && !invertMatch {
+ delete(patterns, k)
+ }
}
}
+
}
if invertMatch {
@@ -384,7 +422,8 @@ func init() {
grepCmd.Flags().BoolP("delete-matched", "", false, "delete a pattern right after being matched, this keeps the firstly matched data and speedups when using regular expressions")
grepCmd.Flags().BoolP("invert-match", "v", false, "invert the sense of matching, to select non-matching records")
grepCmd.Flags().BoolP("by-name", "n", false, "match by full name instead of just ID")
- grepCmd.Flags().BoolP("by-seq", "s", false, "search subseq on seq, only positive strand is searched, and mismatch allowed using flag -m/--max-mismatch")
+ grepCmd.Flags().BoolP("by-seq", "s", false, "search subseq on seq, both positive and negative strand are searched, and mismatch allowed using flag -m/--max-mismatch")
+ grepCmd.Flags().BoolP("only-positive-strand", "P", false, "only search on positive strand")
grepCmd.Flags().IntP("max-mismatch", "m", 0, "max mismatch when matching by seq. For large genomes like human genome, using mapping/alignment tools would be faster")
grepCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
grepCmd.Flags().BoolP("degenerate", "d", false, "pattern/motif contains degenerate base")
=====================================
seqkit/cmd/locate.go
=====================================
@@ -41,20 +41,23 @@ var locateCmd = &cobra.Command{
Short: "locate subsequences/motifs, mismatch allowed",
Long: `locate subsequences/motifs, mismatch allowed
-Motifs could be EITHER plain sequence containing "ACTGN" OR regular
-expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
-Degenerate bases like "RYMM.." are also supported by flag -d.
-
-By default, motifs are treated as regular expression.
-When flag -d given, regular expression may be wrong.
-For example: "\w" will be wrongly converted to "\[AT]".
-
-Mismatch is allowed using flag "-m/--max-mismatch",
-but it's not fast enough for large genome like human genome.
-Though, it's fast enough for microbial genomes.
-
-When using flag --circular, end position of matched subsequence that
-crossing genome sequence end would be greater than sequence length.
+Attentions:
+
+ 1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
+ expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
+ 2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+ But do not use degenerate bases/residues in regular expression, you need
+ convert them to regular expression, e.g., change "N" or "X" to "."..
+ 3. When providing search patterns (motifs) via flag '-p',
+ please use double quotation marks for patterns containing comma,
+ e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+ parser accepts comma-separated-values (CSV) for multiple values (motifs).
+ Patterns in file do not follow this rule.
+ 4. Mismatch is allowed using flag "-m/--max-mismatch",
+ but it's not fast enough for large genome like human genome.
+ Though, it's fast enough for microbial genomes.
+ 5. When using flag --circular, end position of matched subsequence that
+ crossing genome sequence end would be greater than sequence length.
`,
Run: func(cmd *cobra.Command, args []string) {
@@ -89,6 +92,10 @@ crossing genome sequence end would be greater than sequence length.
hideMatched := getFlagBool(cmd, "hide-matched")
circular := getFlagBool(cmd, "circular")
+ if config.Alphabet == seq.Protein {
+ onlyPositiveStrand = true
+ }
+
if len(pattern) == 0 && patternFile == "" {
checkError(fmt.Errorf("one of flags -p (--pattern) and -f (--pattern-file) needed"))
}
@@ -209,6 +216,7 @@ crossing genome sequence end would be greater than sequence length.
}
re, err := regexp.Compile(s)
checkError(err)
+ fmt.Println(s, re)
regexps[p] = re
} else if bytes.Index(patterns[p], []byte(".")) >= 0 ||
!(seq.DNAredundant.IsValid(patterns[p]) == nil ||
=====================================
seqkit/cmd/seq.go
=====================================
@@ -42,6 +42,10 @@ var seqCmd = &cobra.Command{
Short: "transform sequences (revserse, complement, extract ID...)",
Long: `transform sequences (revserse, complement, extract ID...)
+Attentions:
+
+ 1. This command outputs plain text even when out file ends with ".gz".
+
`,
Run: func(cmd *cobra.Command, args []string) {
config := getConfigs(cmd)
=====================================
seqkit/cmd/shuffle.go
=====================================
@@ -216,7 +216,6 @@ Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.
sequence := subseqByFaixNotCleaned(faidx, chr, r, 1, -1)
outfh.Write([]byte(fmt.Sprintf(">%s\n", chr)))
outfh.Write(sequence)
- outfh.WriteString("\n")
}
if (isStdin(file) || !isPlainFile(file)) && !keepTemp {
=====================================
seqkit/cmd/split2.go
=====================================
@@ -90,9 +90,13 @@ according to the input files.
force := getFlagBool(cmd, "force")
if size == 0 && parts == 0 && length == 0 {
- checkError(fmt.Errorf(`one of flags should be given: -s/-p. type "seqkit split2 -h" for help`))
+ checkError(fmt.Errorf(`one of flags should be given: -s/-p/-l. type "seqkit split2 -h" for help`))
}
+ bySize := size > 0
+ byParts := parts > 0
+ byLength := length > 0
+
if parts >= 1000 {
log.Warningf(`value of -p/--parts > 1000 may cause error of "too many open files"`)
}
@@ -134,9 +138,9 @@ according to the input files.
if !quiet {
log.Infof("split seqs from %s", source)
- if size > 0 {
+ if bySize {
log.Infof("split into %d seqs per file", size)
- } else if parts > 0 {
+ } else if byParts {
log.Infof("split into %d parts", parts)
} else {
log.Infof("split by sequence length: %s", lengthS)
@@ -192,23 +196,24 @@ according to the input files.
var counts []int
var outfiles []string
- if size > 0 || length > 0 { // by size or by length
+ 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 parts > 0 { // by part
+ } else if byParts { // by part
outfhs = make([]*xopen.Writer, 0, parts)
counts = make([]int, 0, parts)
outfiles = make([]string, 0, parts)
} else {
- checkError(fmt.Errorf(`one of flags should be given: -s/-p. type "seqkit split2 -h" for help`))
+ checkError(fmt.Errorf(`one of flags should be given: -s/-p/-l. type "seqkit split2 -h" for help`))
}
- var outfh *xopen.Writer
fastxReader, err = fastx.NewReader(alphabet, file, idRegexp)
checkError(err)
- i := 0 // nth part
- j := 0 // nth record
+ i := 0 // nth part
+ j := 0
var n int64 // length sum
for {
record, err = fastxReader.Read()
@@ -219,6 +224,7 @@ according to the input files.
checkError(err)
break
}
+
if fastxReader.IsFastq {
config.LineWidth = 0
fastx.ForcelyOutputFastq = true
@@ -234,7 +240,7 @@ according to the input files.
}
n += int64(len(record.Seq.Seq))
- if size > 0 {
+ if bySize {
if j == size {
outfhs[i].Close()
if !quiet {
@@ -254,25 +260,55 @@ according to the input files.
j = 0
}
- } else if length > 0 {
+ } else if byLength {
+ flag = false
if n >= length {
- outfhs[i].Close()
- if !quiet {
- log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+ 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
+ } 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
}
- 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
+ flag = false
+ } else { // write this record later
+ flag = true
}
}
@@ -286,15 +322,20 @@ according to the input files.
counts = append(counts, 0)
outfiles = append(outfiles, outfile)
}
- outfh = outfhs[i]
- record.FormatToWriter(outfh, config.LineWidth)
-
- counts[i]++
+ if byLength {
+ if flag {
+ record.FormatToWriter(outfhs[i], config.LineWidth)
+ counts[i]++
+ }
+ } else {
+ record.FormatToWriter(outfhs[i], config.LineWidth)
+ counts[i]++
+ }
- if size > 0 {
+ if bySize {
j++ // increase size
- } else if parts > 0 {
+ } else if byParts {
i++
if i == parts { // reset index
i = 0
@@ -304,15 +345,20 @@ according to the input files.
}
}
- // for by-size/length: only log last part,
+ // for by-size: only log last part,
// for by-parts: log all parts.
for i, outfh := range outfhs {
- if outfh != nil {
- outfh.Close()
+ if outfh == nil {
+ continue
}
+ outfh.Close()
if !quiet {
- log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+ if counts[i] == 0 {
+ os.Remove(outfiles[i])
+ } else {
+ log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+ }
}
}
@@ -330,7 +376,7 @@ func init() {
split2Cmd.Flags().StringP("read2", "2", "", "(gzipped) read2 file")
split2Cmd.Flags().IntP("by-size", "s", 0, "split sequences into multi parts with N sequences")
split2Cmd.Flags().IntP("by-part", "p", 0, "split sequences into N parts")
- split2Cmd.Flags().StringP("by-length", "l", "", "split sequences into chunks of N bases, supports K/M/G suffix")
+ split2Cmd.Flags().StringP("by-length", "l", "", "split sequences into chunks of >=N bases, supports K/M/G suffix")
split2Cmd.Flags().StringP("out-dir", "O", "", "output directory (default value is $infile.split)")
split2Cmd.Flags().BoolP("force", "f", false, "overwrite output directory")
}
=====================================
seqkit/cmd/version.go
=====================================
@@ -29,7 +29,7 @@ import (
)
// VERSION of seqkit
-const VERSION = "0.14.0"
+const VERSION = "0.15.0"
// versionCmd represents the version command
var versionCmd = &cobra.Command{
=====================================
seqkit/packaging.sh
=====================================
@@ -1,6 +1,6 @@
#!/usr/bin/env sh
-CGO_ENABLED=0 gox -os="windows darwin linux" -arch="386 amd64" -tags netgo -ldflags '-w -s' -asmflags '-trimpath'
+CGO_ENABLED=0 gox -os="windows darwin linux" -arch="386 amd64 arm64" -tags netgo -ldflags '-w -s' -asmflags '-trimpath'
dir=binaries
mkdir -p $dir;
=====================================
tests/test.sh
=====================================
@@ -605,7 +605,7 @@ fun(){
SCAT_PID=$!
BAK=$IFS
IFS=$'\n'
- SIZE=3
+ SIZE=2
for i in `seq 0 $SIZE`;
do
for j in `seq 0 $SIZE`;
@@ -652,7 +652,7 @@ fun(){
SCAT_PID=$!
BAK=$IFS
IFS=$'\n'
- SIZE=3
+ SIZE=2
for i in `seq 0 $SIZE`;
do
for j in `seq 0 $SIZE`;
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/cafbc21b5e1338d2828face33bb06401b31e3193...6d3823658c702f7a0599d69b2e7f888de4158f9f
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/cafbc21b5e1338d2828face33bb06401b31e3193...6d3823658c702f7a0599d69b2e7f888de4158f9f
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