[med-svn] [Git][med-team/seqkit][master] 5 commits: New upstream version 0.12.1+ds
Nilesh Patra
gitlab at salsa.debian.org
Mon Aug 3 15:00:06 BST 2020
Nilesh Patra pushed to branch master at Debian Med / seqkit
Commits:
fdab9ef8 by Nilesh Patra at 2020-08-03T18:29:56+05:30
New upstream version 0.12.1+ds
- - - - -
1173ccfb by Nilesh Patra at 2020-08-03T18:30:28+05:30
Update upstream source from tag 'upstream/0.12.1+ds'
Update to upstream version '0.12.1+ds'
with Debian dir 6ed0ab594a77ea01f4ab7064d95730af53b73c85
- - - - -
a51b6bed by Nilesh Patra at 2020-08-03T18:31:16+05:30
Repack to remove generated files
- - - - -
e6e87bf3 by Nilesh Patra at 2020-08-03T19:17:15+05:30
Add manpages
- - - - -
2c2feb26 by Nilesh Patra at 2020-08-03T19:27:23+05:30
Fix spellings
- - - - -
16 changed files:
- − benchmark/revcom_biogo
- debian/changelog
- debian/copyright
- + debian/createmanpages
- + debian/manpages
- debian/patches/series
- + debian/patches/spellings.patch
- + debian/seqkit-benchmark.1
- + debian/seqkit.1
- debian/watch
- − tests/pcs109_5k.bam
- − tests/pcs109_5k.bam.bai
- − tests/pcs109_5k_prim.bam
- − tests/pcs109_5k_prim.bam.bai
- − tests/pcs109_5k_spliced.bam
- − tests/pcs109_5k_spliced.bam.bai
Changes:
=====================================
benchmark/revcom_biogo deleted
=====================================
Binary files a/benchmark/revcom_biogo and /dev/null differ
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-seqkit (0.12.1-1) UNRELEASED; urgency=medium
+seqkit (0.12.1+ds-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
TODO: https://salsa.debian.org/go-team/packages/golang-github-biogo-biogo
=====================================
debian/copyright
=====================================
@@ -1,6 +1,8 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: SeqKit
Source: https://github.com/shenwei356/seqkit/releases
+Files-Excluded: benchmark/revcom_biogo
+ tests/*.bam*
Files: *
Copyright: 2016-2020 Wei Shen, 2019 Oxford Nanopore Technologies.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,45 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=seqkit
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=seqkit-benchmark
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
use-upstream-go-logger.patch
+spellings.patch
=====================================
debian/patches/spellings.patch
=====================================
@@ -0,0 +1,168 @@
+Author: Nilesh Patra <npatra974 at gmail.com>
+Description: Fix spellings in the package
+Last Changed: August 3, 2020
+--- a/seqkit/cmd/bam.go
++++ b/seqkit/cmd/bam.go
+@@ -754,14 +754,14 @@
+ }
+
+ fmap["RefAln"] = fieldInfo{
+- "Aligned refence length",
++ "Aligned reference length",
+ func(r *sam.Record) float64 {
+ return float64(r.Len())
+ },
+ }
+
+ fmap["RefCov"] = fieldInfo{
+- "Refence coverage",
++ "Reference coverage",
+ func(r *sam.Record) float64 {
+ return float64(r.Len()) / float64(r.Ref.Len()) * 100
+ },
+--- a/seqkit/cmd/faidx.go
++++ b/seqkit/cmd/faidx.go
+@@ -205,7 +205,7 @@
+ func init() {
+ RootCmd.AddCommand(faidxCmd)
+
+- faidxCmd.Flags().BoolP("use-regexp", "r", false, "IDs are regular expression. But subseq region is not suppored here.")
++ faidxCmd.Flags().BoolP("use-regexp", "r", false, "IDs are regular expression. But subseq region is not supported here.")
+ faidxCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
+ faidxCmd.Flags().BoolP("full-head", "f", false, "print full header line instead of just ID. New fasta index file ending with .seqkit.fai will be created")
+
+--- a/seqkit/cmd/mutate.go
++++ b/seqkit/cmd/mutate.go
+@@ -43,7 +43,7 @@
+
+ Attentions:
+
+- 1. Mutiple point mutations (-p/--point) are allowed, but only single
++ 1. Multiple point mutations (-p/--point) are allowed, but only single
+ insertion (-i/--insertion) OR single deletion (-d/--deletion) is allowed.
+ 2. Point mutation takes place before insertion/deletion.
+
+--- a/seqkit/cmd/replace.go
++++ b/seqkit/cmd/replace.go
+@@ -220,7 +220,7 @@
+ "ATTENTION: for *nix OS, use SINGLE quote NOT double quotes or "+
+ `use the \ escape character. Record number is also supported by "{nr}".`+
+ `use ${1} instead of $1 when {kv} given!`)
+- replaceCmd.Flags().IntP("nr-width", "", 1, `minimum width for {nr} in flag -r/--replacement. e.g., formating "1" to "001" by --nr-width 3`)
++ replaceCmd.Flags().IntP("nr-width", "", 1, `minimum width for {nr} in flag -r/--replacement. e.g., formatting "1" to "001" by --nr-width 3`)
+ // replaceCmd.Flags().BoolP("by-name", "n", false, "replace full name instead of just id")
+ replaceCmd.Flags().BoolP("by-seq", "s", false, "replace seq")
+ replaceCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
+--- a/seqkit/cmd/root.go
++++ b/seqkit/cmd/root.go
+@@ -62,7 +62,7 @@
+ }
+ RootCmd.PersistentFlags().StringP("seq-type", "t", "auto", "sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence)")
+ RootCmd.PersistentFlags().IntP("threads", "j", defaultThreads, "number of CPUs. (default value: 1 for single-CPU PC, 2 for others)")
+- RootCmd.PersistentFlags().IntP("line-width", "w", 60, "line width when outputing FASTA format (0 for no wrap)")
++ RootCmd.PersistentFlags().IntP("line-width", "w", 60, "line width when outputting FASTA format (0 for no wrap)")
+ RootCmd.PersistentFlags().StringP("id-regexp", "", fastx.DefaultIDRegexp, "regular expression for parsing ID")
+ RootCmd.PersistentFlags().BoolP("id-ncbi", "", false, "FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud...")
+ RootCmd.PersistentFlags().StringP("out-file", "o", "-", `out file ("-" for stdout, suffix .gz for gzipped out)`)
+--- a/seqkit/cmd/shuffle.go
++++ b/seqkit/cmd/shuffle.go
+@@ -46,7 +46,7 @@
+ supported.
+
+ Firstly, seqkit reads the sequence IDs. If the file is not plain FASTA file,
+-seqkit will write the sequences to tempory files, and create FASTA index.
++seqkit will write the sequences to temporary files, and create FASTA index.
+
+ Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.
+
+@@ -149,7 +149,7 @@
+ newFile = file + ".fastx"
+ }
+ if !quiet {
+- log.Infof("read and write sequences to tempory file: %s ...", newFile)
++ log.Infof("read and write sequences to temporary file: %s ...", newFile)
+ }
+
+ var nseqs int
+@@ -231,5 +231,5 @@
+ 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)")
+- shuffleCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")
++ shuffleCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")
+ }
+--- a/seqkit/cmd/sort.go
++++ b/seqkit/cmd/sort.go
+@@ -50,7 +50,7 @@
+
+ Firstly, seqkit reads the sequence head and length information.
+ If the file is not plain FASTA file,
+-seqkit will write the sequences to tempory files, and create FASTA index.
++seqkit will write the sequences to temporary files, and create FASTA index.
+
+ Secondly, seqkit sorts sequence by head and length information
+ and extracts sequences by FASTA index.
+@@ -240,7 +240,7 @@
+ newFile = file + ".fastx"
+ }
+ if !quiet {
+- log.Infof("read and write sequences to tempory file: %s ...", newFile)
++ log.Infof("read and write sequences to temporary file: %s ...", newFile)
+ }
+
+ var nseqs int
+@@ -440,6 +440,6 @@
+ sortCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
+
+ sortCmd.Flags().BoolP("two-pass", "2", false, "two-pass mode read files twice to lower memory usage. (only for FASTA format)")
+- sortCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")
++ sortCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")
+ sortCmd.Flags().IntP("seq-prefix-length", "L", 10000, "length of sequence prefix on which seqkit sorts by sequences (0 for whole sequence)")
+ }
+--- a/seqkit/cmd/split.go
++++ b/seqkit/cmd/split.go
+@@ -195,7 +195,7 @@
+ newFile = file + ".fastx"
+ }
+ if !quiet {
+- log.Infof("read and write sequences to tempory file: %s ...", newFile)
++ log.Infof("read and write sequences to temporary file: %s ...", newFile)
+ }
+
+ var nseqs int
+@@ -361,7 +361,7 @@
+ newFile = file + ".fastx"
+ }
+ if !quiet {
+- log.Infof("read and write sequences to tempory file: %s ...", newFile)
++ log.Infof("read and write sequences to temporary file: %s ...", newFile)
+ }
+
+ var nseqs int
+@@ -530,7 +530,7 @@
+ newFile = file + ".fastx"
+ }
+ if !quiet {
+- log.Infof("read and write sequences to tempory file: %s ...", newFile)
++ log.Infof("read and write sequences to temporary file: %s ...", newFile)
+ }
+
+ var nseqs int
+@@ -721,7 +721,7 @@
+ newFile = file + ".fastx"
+ }
+ if !quiet {
+- log.Infof("read and write sequences to tempory file: %s ...", newFile)
++ log.Infof("read and write sequences to temporary file: %s ...", newFile)
+ }
+
+ var nseqs int
+@@ -853,7 +853,7 @@
+ `e.g 1:12 for first 12 bases, -12:-1 for last 12 bases. type "seqkit split -h" for more examples`)
+ splitCmd.Flags().BoolP("two-pass", "2", false, "two-pass mode read files twice to lower memory usage. (only for FASTA format)")
+ splitCmd.Flags().BoolP("dry-run", "d", false, "dry run, just print message and no files will be created.")
+- splitCmd.Flags().BoolP("keep-temp", "k", false, "keep tempory FASTA and .fai file when using 2-pass mode")
++ splitCmd.Flags().BoolP("keep-temp", "k", false, "keep temporary FASTA and .fai file when using 2-pass mode")
+ splitCmd.Flags().StringP("out-dir", "O", "", "output directory (default value is $infile.split)")
+ splitCmd.Flags().BoolP("force", "f", false, "overwrite output directory")
+ }
=====================================
debian/seqkit-benchmark.1
=====================================
@@ -0,0 +1,8 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH SEQKIT-BENCHMARK "1" "August 2020" "seqkit-benchmark 0.12.1+ds" "User Commands"
+.SH NAME
+seqkit-benchmark \- cross-platform and ultrafast toolkit for FASTA/Q file manipulation
+.SH DESCRIPTION
+feed me one uncompressed FASTA file
+.SH USAGE
+seqkit-benchmark <fasta-file>
=====================================
debian/seqkit.1
=====================================
@@ -0,0 +1,107 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH SEQKIT "1" "August 2020" "seqkit 0.12.1+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: 0.12.1
+.PP
+Author: Wei Shen <shenwei356 at gmail.com>
+.PP
+Documents : http://bioinf.shenwei.me/seqkit
+Source code: https://github.com/shenwei356/seqkit
+Please cite: https://doi.org/10.1371/journal.pone.0163962
+.SS "Usage:"
+.IP
+seqkit [command]
+.SS "Available Commands:"
+.TP
+amplicon
+retrieve amplicon (or specific region around it) via primer(s)
+.TP
+bam
+monitoring and online histograms of BAM record features
+.TP
+common
+find common sequences of multiple files by id/name/sequence
+.TP
+concat
+concatenate sequences with same ID from multiple files
+.TP
+convert
+convert FASTQ quality encoding between Sanger, Solexa and Illumina
+.TP
+duplicate
+duplicate sequences N times
+.TP
+faidx
+create FASTA index file and extract subsequence
+.TP
+fish
+look for short sequences in larger sequences using local alignment
+.TP
+fq2fa
+convert FASTQ to FASTA
+.TP
+fx2tab
+convert FASTA/Q to tabular format (with length/GC content/GC skew)
+.IP
+genautocomplete generate shell autocompletion script
+grep search sequences by ID/name/sequence/sequence motifs, mismatch allowed
+head print first N FASTA/Q records
+help Help about any command
+locate locate subsequences/motifs, mismatch allowed
+mutate edit sequence (point mutation, insertion, deletion)
+range print FASTA/Q records in a range (start:end)
+rename rename duplicated IDs
+replace replace name/sequence by regular expression
+restart reset start position for circular genome
+rmdup remove duplicated sequences by id/name/sequence
+sample sample sequences by number or proportion
+sana sanitize broken single line fastq files
+seq transform sequences (revserse, complement, extract ID...)
+shuffle shuffle sequences
+sliding sliding sequences, circular genome supported
+sort sort sequences by id/name/sequence/length
+split split sequences into files by id/seq region/size/parts (mainly for FASTA)
+split2 split sequences into files by size/parts (FASTA, PE/SE FASTQ)
+stats simple statistics of FASTA/Q files
+subseq get subsequences by region/gtf/bed, including flanking sequences
+tab2fx convert tabular format to FASTA/Q format
+translate translate DNA/RNA to protein sequence (supporting ambiguous bases)
+version print version information and check for update
+watch monitoring and online histograms of sequence features
+.SS "Flags:"
+.TP
+\fB\-\-alphabet\-guess\-seq\-length\fR int
+length of sequence prefix of the first FASTA record based on which seqkit guesses the sequence type (0 for whole seq) (default 10000)
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+help for seqkit
+.TP
+\fB\-\-id\-ncbi\fR
+FASTA head is NCBI\-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud...
+.TP
+\fB\-\-id\-regexp\fR string
+regular expression for parsing ID (default "^(\e\eS+)\e\es?")
+.TP
+\fB\-\-infile\-list\fR string
+file of input files list (one file per line), if given, they are appended to files from cli arguments
+.TP
+\fB\-w\fR, \fB\-\-line\-width\fR int
+line width when outputting FASTA format (0 for no wrap) (default 60)
+.TP
+\fB\-o\fR, \fB\-\-out\-file\fR string
+out file ("\-" for stdout, suffix .gz for gzipped out) (default "\-")
+.TP
+\fB\-\-quiet\fR
+be quiet and do not show extra information
+.TP
+\fB\-t\fR, \fB\-\-seq\-type\fR string
+sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence) (default "auto")
+.TP
+\fB\-j\fR, \fB\-\-threads\fR int
+number of CPUs. (default value: 1 for single\-CPU PC, 2 for others) (default 2)
+.PP
+Use "seqkit [command] \fB\-\-help\fR" for more information about a command.
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%,repacksuffix=+ds,dversionmangle=auto" \
https://github.com/shenwei356/seqkit/releases .*/archive/v?@ANY_VERSION@\.tar\.gz
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=====================================
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View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/0f4214b943a7a5ed851da9beed99d560634a1afb...2c2feb26d8ef4fcd2a031b0000a55afe731027d6
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