[med-svn] [python-pyfaidx] 01/02: Add examples package and manpage
Andreas Tille
tille at debian.org
Tue Oct 20 08:36:51 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-pyfaidx.
commit 45fe6cedc74cbb75f478160eb19944d05ba577e6
Author: Andreas Tille <tille at debian.org>
Date: Tue Oct 20 10:14:47 2015 +0200
Add examples package and manpage
---
debian/control | 21 ++++++++-
debian/faidx.1 | 84 +++++++++++++++++++++++++++++++++
debian/python-pyfaidx-examples.examples | 1 +
debian/python3-pyfaidx.manpages | 1 +
debian/rules | 5 ++
5 files changed, 110 insertions(+), 2 deletions(-)
diff --git a/debian/control b/debian/control
index e9253d8..4f95ea9 100644
--- a/debian/control
+++ b/debian/control
@@ -29,7 +29,7 @@ Description: efficient random access to fasta subsequences for Python
Samtools provides a function "faidx" (FAsta InDeX), which creates a
small flat index file ".fai" allowing for fast random access to any
subsequence in the indexed FASTA file, while loading a minimal amount of
- the file in to memory. This python module implements pure Python classes
+ the file in to memory. This Python module implements pure Python classes
for indexing, retrieval, and in-place modification of FASTA files using
a samtools compatible index. The pyfaidx module is API compatible with
the pygr seqdb module. A command-line script "faidx" is installed
@@ -46,7 +46,7 @@ Description: efficient random access to fasta subsequences for Python 3
Samtools provides a function "faidx" (FAsta InDeX), which creates a
small flat index file ".fai" allowing for fast random access to any
subsequence in the indexed FASTA file, while loading a minimal amount of
- the file in to memory. This python module implements pure Python classes
+ the file in to memory. This Python module implements pure Python classes
for indexing, retrieval, and in-place modification of FASTA files using
a samtools compatible index. The pyfaidx module is API compatible with
the pygr seqdb module. A command-line script "faidx" is installed
@@ -54,3 +54,20 @@ Description: efficient random access to fasta subsequences for Python 3
FASTA files without any programming knowledge.
.
This package provides the Python 3 modules to access fasta files.
+
+Package: python-pyfaidx-examples
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: python3-pyfaidx | python-pyfaidx
+Description: example data for efficient random access to fasta subsequences for Python
+ Samtools provides a function "faidx" (FAsta InDeX), which creates a
+ small flat index file ".fai" allowing for fast random access to any
+ subsequence in the indexed FASTA file, while loading a minimal amount of
+ the file in to memory. This Python module implements pure Python classes
+ for indexing, retrieval, and in-place modification of FASTA files using
+ a samtools compatible index. The pyfaidx module is API compatible with
+ the pygr seqdb module. A command-line script "faidx" is installed
+ alongside the pyfaidx module, and facilitates complex manipulation of
+ FASTA files without any programming knowledge.
+ .
+ This package provides example data to test the Python modules.
diff --git a/debian/faidx.1 b/debian/faidx.1
new file mode 100644
index 0000000..2b6bac2
--- /dev/null
+++ b/debian/faidx.1
@@ -0,0 +1,84 @@
+.TH FAIDX "1" "October 2015" "faidx 0.4.2" "User Commands"
+.SH NAME
+faidx \- Fetch sequences from FASTA
+.SH SYNOPSIS
+.B faidx
+[\-h] [\-b BED] [\-o OUT]
+[\-i {bed,chromsizes,nucleotide,transposed}] [\-c] [\-r] [\-n | \fB\-f]\fR
+[\-x] [\-l] [\-s DEFAULT_SEQ] [\-d DELIMITER] [\-g REGEX] [\-m | \fB\-M]\fR
+[\-\-version]
+fasta [regions [regions ...]]
+.SH DESCRIPTION
+Fetch sequences from FASTA. If no regions are specified, all entries in the
+input file are returned. Input FASTA file must be consistently line\-wrapped,
+and line wrapping of output is based on input line lengths.
+.SH OPTIONS
+.SS Positional arguments
+.TP
+fasta
+FASTA file
+.TP
+regions
+space separated regions of sequence to fetch e.g.
+chr1:1\-1000
+.SS Optional arguments
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-b\fR BED, \fB\-\-bed\fR BED
+bed file of regions
+.TP
+\fB\-o\fR OUT, \fB\-\-out\fR OUT
+output file name (default: stdout)
+.TP
+\fB\-i\fR {bed,chromsizes,nucleotide,transposed}, \fB\-\-transform\fR {bed,chromsizes,nucleotide,transposed}
+transform the requested regions into another format.
+default: None
+.TP
+\fB\-c\fR, \fB\-\-complement\fR
+complement the sequence. default: False
+.TP
+\fB\-r\fR, \fB\-\-reverse\fR
+reverse the sequence. default: False
+.TP
+\fB\-n\fR, \fB\-\-no\-names\fR
+omit sequence names from output. default: False
+.TP
+\fB\-f\fR, \fB\-\-full\-names\fR
+output full names including description. default:
+False
+.TP
+\fB\-x\fR, \fB\-\-split\-files\fR
+write each region to a separate file (names are
+derived from regions)
+.TP
+\fB\-l\fR, \fB\-\-lazy\fR
+fill in \fB\-\-default\-seq\fR for missing ranges. default:
+False
+.TP
+\fB\-s\fR DEFAULT_SEQ, \fB\-\-default\-seq\fR DEFAULT_SEQ
+default base for missing positions and masking.
+default: N
+.TP
+\fB\-d\fR DELIMITER, \fB\-\-delimiter\fR DELIMITER
+delimiter for splitting names to multiple values
+(duplicate names will be discarded). default: None
+.TP
+\fB\-g\fR REGEX, \fB\-\-regex\fR REGEX
+regular expression for filtering non\-matching sequence
+names. default: .*
+.TP
+\fB\-m\fR, \fB\-\-mask\-with\-default\-seq\fR
+mask the FASTA file using \fB\-\-default\-seq\fR default: False
+.TP
+\fB\-M\fR, \fB\-\-mask\-by\-case\fR
+mask the FASTA file by changing to lowercase. default:
+False
+.TP
+\fB\-\-version\fR
+print pyfaidx version number
+.SH SEE ALSO
+Please cite: Shirley MD, Ma Z, Pedersen BS, Wheelan SJ. (2015) Efficient
+"pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e1196
+https://dx.doi.org/10.7287/peerj.preprints.970v1
diff --git a/debian/python-pyfaidx-examples.examples b/debian/python-pyfaidx-examples.examples
new file mode 100644
index 0000000..b806c7a
--- /dev/null
+++ b/debian/python-pyfaidx-examples.examples
@@ -0,0 +1 @@
+tests/data/[abce-z]*
diff --git a/debian/python3-pyfaidx.manpages b/debian/python3-pyfaidx.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/python3-pyfaidx.manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/rules b/debian/rules
index a48107d..fc28cea 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,6 +9,11 @@ export PYBUILD_NAME=pyfaidx
%:
dh $@ --with python2,python3 --buildsystem=pybuild
+override_dh_install:
+ dh_install
+ # remove duplilcated wrapper script from Python2 package
+ rm -rf debian/python-$(PYBUILD_NAME)/usr/bin
+
override_dh_auto_test:
LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom --test-args='set -e; \
{interpreter} -m "nose" --with-coverage --cover-package=pyfaidx'
--
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