[med-svn] [Git][med-team/htseq][master] 6 commits: Binaries are provided in python3-htseq package
Andreas Tille
gitlab at salsa.debian.org
Tue May 1 10:58:11 BST 2018
Andreas Tille pushed to branch master at Debian Med / htseq
Commits:
4dc606ec by Andreas Tille at 2018-05-01T11:18:52+02:00
Binaries are provided in python3-htseq package
- - - - -
aa30f621 by Andreas Tille at 2018-05-01T11:23:17+02:00
hardening=+all
- - - - -
02104107 by Andreas Tille at 2018-05-01T11:25:41+02:00
Provide manpages from old version (FIXME: Needs verification whether it is correct for new version)
- - - - -
bdbd3b76 by Andreas Tille at 2018-05-01T11:29:37+02:00
Secure URI in watch file (pointing to new PyPi)
- - - - -
eb09d4b9 by Andreas Tille at 2018-05-01T11:35:50+02:00
Fix spelling
- - - - -
ca680705 by Andreas Tille at 2018-05-01T11:36:25+02:00
Testsuite: autopkgtest-pkg-python
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/man/htseq-count.1
- + debian/man/htseq-qa.1
- + debian/python3-htseq.manpages
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-htseq (0.9.1-1) UNRELEASED; urgency=medium
+htseq (0.9.1-1) unstable; urgency=medium
* New upstream version
* Point Vcs fields to salsa.debian.org
@@ -8,8 +8,13 @@ htseq (0.9.1-1) UNRELEASED; urgency=medium
- Remove unused get-orig-source target
- There is no clean script any more so remove the specific targets
* Sphinx doc does not seem to reported any more
+ * Provide Python3 package
+ * Binaries are provided in python3-htseq package
+ * hardening=+all
+ * Secure URI in watch file (pointing to new PyPi)
+ * Testsuite: autopkgtest-pkg-python
- -- Andreas Tille <tille at debian.org> Tue, 01 May 2018 07:49:00 +0200
+ -- Andreas Tille <tille at debian.org> Tue, 01 May 2018 11:29:55 +0200
htseq (0.6.1p1-4) unstable; urgency=medium
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,6 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Diane Trout <diane at ghic.org>,
Andreas Tille <tille at debian.org>
Section: python
+Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper (>= 11~),
python-debian,
@@ -52,7 +53,7 @@ Depends: ${misc:Depends},
${python3:Depends},
${shlibs:Depends}
Breaks: python-htseq (<= 0.9.1)
-Provides: python-htseq (<= 0.9.1)
+Provides: python-htseq
Description: Python3 high-throughput genome sequencing read analysis utilities
HTSeq can be used to performing a number of common analysis tasks
when working with high-throughput genome sequencing reads:
=====================================
debian/man/htseq-count.1
=====================================
--- /dev/null
+++ b/debian/man/htseq-count.1
@@ -0,0 +1,317 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "HTSEQ-COUNT" "1" "Oct 01, 2017" "0.6.1p1" "HTSeq"
+.SH NAME
+htseq-count \- Count the number of reads in a SAM alignment file that map to GFF features
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+Given a file with aligned sequencing reads and a list of genomic
+features, a common task is to count how many reads map to each feature.
+.sp
+A feature is here an interval (i.e., a range of positions) on a chromosome
+or a union of such intervals.
+.sp
+In the case of RNA\-Seq, the features are typically genes, where each gene
+is considered here as the union of all its exons. One may also consider
+each exon as a feature, e.g., in order to check for alternative splicing.
+For comparative ChIP\-Seq, the features might be binding region from a
+pre\-determined list.
+.sp
+Special care must be taken to decide how to deal with reads that overlap more
+than one feature. The \fBhtseq\-count\fP script allows one to choose between three
+modes. Of course, if none of these fits your needs, you can write your own
+script with HTSeq. See the chapter tour for a step\-by\-step guide on
+how to do so. See also the FAQ at the end, if the following explanation seems
+to technical.
+.sp
+The three overlap resolution modes of \fBhtseq\-count\fP work as follows. For
+each position \fIi\fP in the read, a set \fIS(i)\fP is defined as the set of all
+features overlapping position \fIi\fP\&. Then, consider the set \fIS\fP, which is
+(with \fIi\fP running through all position within the read or a read pair)
+.INDENT 0.0
+.IP \(bu 2
+the union of all the sets \fIS(i)\fP for mode \fBunion\fP\&. This mode is recommended for most use cases.
+.IP \(bu 2
+the intersection of all the sets \fIS(i)\fP for mode \fBintersection\-strict\fP\&.
+.IP \(bu 2
+the intersection of all non\-empty sets \fIS(i)\fP for mode \fBintersection\-nonempty\fP\&.
+.UNINDENT
+.sp
+If \fIS\fP contains precisely one feature, the read (or read pair) is counted for this feature. If
+it contains more than one feature, the read (or read pair) is counted as \fBambiguous\fP (and
+not counted for any features), and if \fBS\fP is empty, the read (or read pair) is counted
+as \fBno_feature\fP\&.
+.sp
+The following figure illustrates the effect of these three modes:
+[image]
+.SH USAGE
+.sp
+After you have installed HTSeq (see install), you can run \fBhtseq\-count\fP from
+the command line:
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+htseq\-count [options] <alignment_file> <gff_file>
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.sp
+If the file \fBhtseq\-qa\fP is not in your path, you can, alternatively, call the script with
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+python \-m HTSeq.scripts.count [options] <alignment_file> <gff_file>
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.sp
+The \fB<alignment_file>\fP contains the aligned reads in the SAM format. (Note that the
+\fI\%SAMtools\fP contain Perl scripts to convert most alignment formats to SAM.)
+Make sure to use a splicing\-aware aligner such as TopHat. HTSeq\-count makes
+full use of the information in the CIGAR field.
+.sp
+To read from standard input, use \fB\-\fP as \fB<alignment_file>\fP\&.
+.sp
+If you have paired\-end data, pay attention to the \fB\-r\fP option described below.
+.sp
+The \fB<gff_file>\fP contains the features in the \fI\%GFF format\fP\&.
+.sp
+The script outputs a table with counts for each feature, followed by
+the special counters, which count reads that were not counted for any feature
+for various reasons. The names of the special counters all start with
+a double underscore, to facilitate filtering. (Note: The double unscore
+was absent up to version 0.5.4). The special counters are:
+.INDENT 0.0
+.IP \(bu 2
+\fB__no_feature\fP: reads (or read pairs) which could not be assigned to any feature
+(set \fIS\fP as described above was empty).
+.IP \(bu 2
+\fB__ambiguous\fP: reads (or read pairs) which could have been assigned to more than
+one feature and hence were not counted for any of these (set \fIS\fP
+had more than one element).
+.IP \(bu 2
+\fB__too_low_aQual\fP: reads (or read pairs) which were skipped due to the \fB\-a\fP
+option, see below
+.IP \(bu 2
+\fB__not_aligned\fP: reads (or read pairs) in the SAM file without alignment
+.IP \(bu 2
+\fB__alignment_not_unique\fP: reads (or read pairs) with more than one reported alignment.
+These reads are recognized from the \fBNH\fP optional SAM field tag.
+(If the aligner does not set this field, multiply aligned reads will
+be counted multiple times, unless they getv filtered out by due to the \fB\-a\fP option.)
+.UNINDENT
+.sp
+\fIImportant:\fP The default for strandedness is \fIyes\fP\&. If your RNA\-Seq data has not been made
+with a strand\-specific protocol, this causes half of the reads to be lost.
+Hence, make sure to set the option \fB\-\-stranded=no\fP unless you have strand\-specific
+data!
+.SS Options
+.INDENT 0.0
+.TP
+.B \-f <format>, \-\-format=<format>
+Format of the input data. Possible values are \fBsam\fP (for text SAM files)
+and \fBbam\fP (for binary BAM files). Default is \fBsam\fP\&.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-r <order>, \-\-order=<order>
+For paired\-end data, the alignment have to be sorted either by read name or
+by alignment position. If your data is not sorted, use the \fBsamtools sort\fP
+function of \fBsamtools\fP to sort it. Use this option, with \fBname\fP or \fBpos\fP
+for \fB<order>\fP to indicate how the input data has been sorted. The default
+is \fBname\fP\&.
+.sp
+If \fBname\fP is indicated, \fBhtseq\-count\fP expects all the alignments for the
+reads of a given read pair to appear in adjacent records in the input data.
+For \fBpos\fP, this is not expected; rather, read alignments whose mate alignment
+have not yet been seen are kept in a buffer in memory until the mate is found.
+While, strictly speaking, the latter will also work with unsorted data, sorting
+ensures that most alignment mates appear close to each other in the data
+and hence the buffer is much less likely to overflow.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-s <yes/no/reverse>, \-\-stranded=<yes/no/reverse>
+whether the data is from a strand\-specific assay (default: \fByes\fP)
+.sp
+For \fBstranded=no\fP, a read is considered overlapping with a feature regardless
+of whether it is mapped to the same or the opposite strand as the feature.
+For \fBstranded=yes\fP and single\-end reads, the read has to be mapped to the same
+strand as the feature. For paired\-end reads, the first
+read has to be on the same strand and the second read on the opposite strand.
+For \fBstranded=reverse\fP, these rules are reversed.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-a <minaqual>, \-\-a=<minaqual>
+skip all reads with alignment quality lower than the given
+minimum value (default: 10 — Note: the default used to be 0 until
+version 0.5.4.)
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-t <feature type>, \-\-type=<feature type>
+feature type (3rd column in GFF file) to be used, all
+features of other type are ignored (default, suitable
+for RNA\-Seq analysis using an \fI\%Ensembl GTF\fP file: \fBexon\fP)
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-i <id attribute>, \-\-idattr=<id attribute>
+GFF attribute to be used as feature ID. Several GFF lines with the same
+feature ID will be considered as parts of the same feature. The feature ID
+is used to identity the counts in the output table. The default, suitable
+for RNA\-Seq analysis using an Ensembl GTF file, is \fBgene_id\fP\&.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-m <mode>, \-\-mode=<mode>
+Mode to handle reads overlapping more than one feature. Possible values for
+\fI<mode>\fP are \fBunion\fP, \fBintersection\-strict\fP and \fBintersection\-nonempty\fP
+(default: \fBunion\fP)
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-o <samout>, \-\-samout=<samout>
+write out all SAM alignment records into an output SAM
+file called <samout>, annotating each line with its
+assignment to a feature or a special counter
+(as an optional field with tag ‘XF’)
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-q, \-\-quiet
+suppress progress report and warnings
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-h, \-\-help
+Show a usage summary and exit
+.UNINDENT
+.SS Frequenctly asked questions
+.INDENT 0.0
+.TP
+.B \fIMy shell reports “command not found” when I try to run “htseq\-count”. How can I launch the script?\fP
+The file “htseq\-count” has to be in the system’s \fI\%search path\fP\&. By default, Python places it
+in its script directory, which you have to add to your search path. A maybe easier alternative
+is to write \fBpython \-m HTSeq.scripts.count\fP instead of \fBhtseq\-count\fP, followed by the
+options and arguments, which will launch the htseq\-count script as well.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \fIWhy are multi\-mapping reads and reads overlapping multiple features discarded rather than counted for each feature?\fP
+The primary intended use case for \fBhtseq\-count\fP is \fIdifferential\fP expression analysis, where
+one compares the expression of the same gene across samples and not the expression of different
+genes within a sample. Now, consider two genes, which share a stretch of common sequence
+such that for a read mapping to this stretch, the aligner cannot decide which of the two genes
+the read originated from and hence reports a multiple alignment. If we discard all such reads,
+we undercount the total output of the genes, but the \fIratio\fP of expression strength (the “fold
+change”) between samples or experimental condition will still be correct, because we discard the
+same fratcion of reads in all samples. On the other hand, if we counted these reads for both
+genes, a subsequent diffential\-expression analysis might find false positives: Even if only one of the
+gene changes increases its expression in reaction to treatment, the additional read caused by this
+would be counted for both genes, giving the wrong appearance that both genes reacted to the treatment.
+.TP
+.B \fII have used a GTF file generated by the Table Browser function of the UCSC Genome Browser, and most reads are counted as ambiguous. Why?\fP
+In these files, the \fBgene_id\fP attribute incorrectly contains the same value as the \fBtranscript_id\fP
+attribute and hence a different value for each transcript of the same gene. Hence, if a read maps to
+an exon shared by several transcripts of the same gene, this will appear to \fBhtseq\-count\fP as and
+overlap with several genes. Therefore, these GTF files cannot be used as is. Either correct the
+incorrect \fBgene_id\fP attributes with a suitable script, or use a GTF file from a different source.
+.TP
+.B \fICan I use htseq\-count to count reads mapping to transcripts rather than genes?\fP
+In principle, you could instruct htseq\-count to count for each of a gene’s transcript individually, by
+specifying \fB\-\-idattr transcript_id\fP\&. However, all reads mapping to exons shared by several
+transcripts will then be considered ambiguous. (See second question.) Counting them for each transcript
+that contains the exons would be possible but makes little sense for typical use cases. (See first
+question.) If you want to perform differential expression analysis on the level of
+individual transcripts, maybe ahve a look at \fI\%our paper on DEXSeq\fP for a discussion on why we
+prefer performing such analyses on the level of exons instead.
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \fIFor paired\-end data, does htseq\-count count reads or read pairs?\fP
+Read pairs. The script is designed to count “units of evidence” for gene expression. If both mates map
+to the same gene, this still only shows that one cDNA fragment originated from that gene. Hence, it
+should be counted only once.
+.TP
+.B \fIWhat happens if the two reads in a pair overlap two different features?\fP
+The same as if one read overlaps two features: The read or read pair is counted as ambiguous.
+.TP
+.B \fIWhat happened if the mate of an aligned read is not aligned?\fP
+For the default mode “union”, only the aligned read determines how the read pair is counted. For the
+other modes, see their description.
+.TP
+.B \fIMost of my RNA\-Seq reads are counted as \(ga\(ga__no_feature\(ga\(ga. What could have gone wrong?\fP
+Common causes include:
+\- The \fB\-\-stranded\fP option was set wrongly. Use a genome browser (e.g., IGV) to check.
+\- The GTF file uses coordinates from another reference assembly as the SAM file.
+\- The chromosome names differ between GTF and SAM file (e.g., \fBchr1\fP in one file and jsut \fB1\fP in the other).
+.TP
+.B \fIWhich overlap mode should I use?\fP
+When I wrote \fBhtseq\-count\fP, I was not sure which option is best and included three possibilities. Now,
+several years later, I have seen very few cases where the default \fBunion\fP would not be appropriate
+and hence tend to recommend to just stick to \fBunion\fP\&.
+.TP
+.B \fII have a GTF file? How do I convert it to GFF?\fP
+No need to do that, because GTF is a tightening of the GFF format. Hence, all GTF files are GFF files, too.
+By default, htseq\-count expects a GTF file.
+.TP
+.B \fII have a GFF file, not a GTF file. How can I use it to count RNA\-Seq reads?\fP
+The GTF format specifies, inter alia, that exons are marked by the word \fBexon\fP in the third column and
+that the gene ID is given in an attribute named \fBgene_id\fP, and htseq\-count expects these words to be used
+by default. If you GFF file uses a word other than \fBexon\fP in its third column to mark lines describing
+exons, notify \fBhtseq\-count\fP using the \fB\-\-type\fP option. If the name of the attribute containing the
+gene ID for exon lines is not \fBgene_id\fP, use the \fB\-\-idattr\fP\&. Often, its is, for example,
+\fBParent\fP, \fBGeneID\fP or \fBID\fP\&. Make sure it is the gene ID and not the exon ID.
+.TP
+.B \fIHow can I count overlaps with features other than genes/exons?\fP
+If you have GFF file listing your features, use it together with the \fB\-\-type\fP and \fB\-\-idattr\fP options.
+If your feature intervals need to be computed, you are probably better off writing your own
+counting script (provided you have some knowledge of Python). Follow the tutorial in the other pages
+of this documentation to see how to use HTSeq for this.
+.TP
+.B \fIHow should I cite htseq\-count in a publication?\fP
+Please cite HTSeq as follows: S Anders, T P Pyl, W Huber: \fIHTSeq — A Python framework to work with
+high\-throughput sequencing data\fP\&. bioRxiv 2014. \fI\%doi: 10.1101/002824\fP\&.
+(This is a preprint currently under review. We will replace this with the reference to the final
+published version once available.)
+.UNINDENT
+.SH AUTHOR
+Simon Anders
+.SH COPYRIGHT
+2017, Simon Anders
+.\" Generated by docutils manpage writer.
+.
=====================================
debian/man/htseq-qa.1
=====================================
--- /dev/null
+++ b/debian/man/htseq-qa.1
@@ -0,0 +1,154 @@
+.\" Man page generated from reStructuredText.
+.
+.TH "HTSEQ-QA" "1" "Oct 01, 2017" "0.6.1p1" "HTSeq"
+.SH NAME
+htseq-qa \- Perform simple quality assessment of high-throughput sequencing reads
+.
+.nr rst2man-indent-level 0
+.
+.de1 rstReportMargin
+\\$1 \\n[an-margin]
+level \\n[rst2man-indent-level]
+level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
+-
+\\n[rst2man-indent0]
+\\n[rst2man-indent1]
+\\n[rst2man-indent2]
+..
+.de1 INDENT
+.\" .rstReportMargin pre:
+. RS \\$1
+. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
+. nr rst2man-indent-level +1
+.\" .rstReportMargin post:
+..
+.de UNINDENT
+. RE
+.\" indent \\n[an-margin]
+.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.nr rst2man-indent-level -1
+.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
+.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
+..
+.sp
+The Python script \fBhtseq\-qa\fP takes a file with sequencing reads (either
+raw or aligned reads) and produces a PDF file with useful plots to assess
+the technical quality of a run.
+.SH PLOT
+.sp
+Here is a typical plot:
+[image]
+.sp
+The plot is made from a SAM file, which contained aligned and unalignable reads.
+The left column is made from the non\-aligned, the right column from the aligned
+reads. The header informs you about the name of the SAM file, and the number of
+reads.
+.sp
+The upper row shows how often which base was called for each position in the
+read. In this sample, the non\-alignable reads have a clear excess in A. The
+aligned reads have a balance between complementing reads: A and C (reddish colours)
+have equal levels, and so do C and G (greenish colours). The sequences seem to be AT
+rich. Furthermore, nearly all aligned reads start with a T, followed by an A, and then,
+a C in 70% and an A in 30% of the reads. Such an imbalance would be reason for concern
+if it has no good explanation. Here, the reason is that the fragmentation of the sample
+was done by enzyme digestion.
+.sp
+The lower half shows the abundance of base\-call quality scores at the different positions
+in the read. Nearly all aligned reads have a quality of 34 over their whole length, while
+for the non\-aligned reads, some reads have lower quality scores towards their ends.
+.SH USAGE
+.sp
+Note that \fBhtseq\-qa\fP needs matplotlib to produce the plot, so you need to install this
+module, as described \fI\%here\fP on the matplotlib web site.
+.sp
+After you have installed HTSeq (see install) and matplotlib, you can run \fBhtseq\-qa\fP from
+the command line:
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+htseq\-qa [options] read_file
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.sp
+If the file \fBhtseq\-qa\fP is not in your path, you can, alternatively, call the script with
+.INDENT 0.0
+.INDENT 3.5
+.sp
+.nf
+.ft C
+python \-m HTSeq.scripts.qa [options] read_file
+.ft P
+.fi
+.UNINDENT
+.UNINDENT
+.sp
+The \fIread_file\fP is either a FASTQ file or a SAM file. For a SAM file, a plot with two columns
+is produced as above, for a FASTQ file, you get only one column.
+.sp
+The output is written into a file with the same name as \fIread_file\fP, with the suffix \fB\&.pdf\fP
+added. View it with a PDF viewer such as the Acrobat Reader.
+.SS Options
+.INDENT 0.0
+.TP
+.B \-t <type>, \-\-type=<type>
+The file type of the \fIread_file\fP\&. Supported values for \fI<type>\fP are:
+.INDENT 7.0
+.IP \(bu 2
+\fBsam\fP: a SAM file (Note that the \fI\%SAMtools\fP contain Perl scripts to convert
+most alignment formats to SAM)
+.IP \(bu 2
+\fBsolexa\-export\fP: an \fB_export.txt\fP file as produced by the SolexaPipeline
+software after aligning with Eland (\fBhtseq\-qa\fP expects the new Solexa quality
+encoding as produced by version 1.3 or newer of the SolexaPipeline)
+.IP \(bu 2
+\fBfastq\fP: a FASTQ file with standard (Sanger or Phred) quality encoding
+.IP \(bu 2
+\fBsolexa\-fastq\fP: a FASTQ file with Solexa quality encoding, as produced by
+the SolexaPipeline after base\-calling with Bustard (\fBhtseq\-qa\fP expects
+the new Solexa quality encoding as produced by version 1.3 or newer
+of the SolexaPipeline)
+.UNINDENT
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-o <outfile>, \-\-outfile=<outfile>
+output filename (default is \fI<read_file>\(ga\(ga\fP\&.pdf\(ga\(ga)
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-r <readlen>, \-\-readlength=<readlen>
+the maximum read length (when not specified, the
+script guesses from the file
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-g <gamma>, \-\-gamma=<gamma>
+the gamma factor for the contrast adjustment of the
+quality score plot
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-n, \-\-nosplit
+do not split reads in unaligned and aligned ones, i.e., produce
+a one\-column plot
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-m, \-\-maxqual
+the maximum quality score that appears in the data (default: 40)
+.UNINDENT
+.INDENT 0.0
+.TP
+.B \-h, \-\-help
+Show a usage summary and exit
+.UNINDENT
+.SH AUTHOR
+Simon Anders
+.SH COPYRIGHT
+2017, Simon Anders
+.\" Generated by docutils manpage writer.
+.
=====================================
debian/python3-htseq.manpages
=====================================
--- /dev/null
+++ b/debian/python3-htseq.manpages
@@ -0,0 +1 @@
+debian/man/*
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -5,6 +5,8 @@ export PYBUILD_NAME=htseq
# see https://wiki.debian.org/Python/LibraryStyleGuide
export http_proxy=http://127.0.9.1:9
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
%:
dh $@ --with python2,python3 --buildsystem=pybuild
@@ -15,3 +17,8 @@ override_dh_auto_clean:
for link in 'src' 'HTSeq' 'doc' 'scripts' 'test' ; do \
if [ -L $${link} ] ; then rm $${link} ; fi \
done
+
+override_dh_install:
+ dh_install
+ # binaries should be only in python3 package
+ rm -rf debian/python-$(PYBUILD_NAME)/usr/bin
\ No newline at end of file
=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,2 @@
-version=3
-http://pypi.debian.net/HTSeq/HTSeq-([0-9.p]*)\.tar\.gz
+version=4
+https://pypi.python.org/pypi/HTSeq .*/HTSeq at ANY_VERSION@@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4
---
View it on GitLab: https://salsa.debian.org/med-team/htseq/compare/1a15a0f9fdf71bda8cfc3359ccba32da18a556af...ca6807052dce671b9c96149b9c0468f9826ef5b4
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