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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
.TH BANDAGE "1" "August 2018" "Bandage 0.8.1" "User Commands"
.SH NAME
Bandage \- Bioinformatics Application for Navigating De novo Assembly Graphs Easily
.SH SYNOPSIS
.B Bandage
\fI\,<command> \/\fR[\fI\,options\/\fR]
.SH DESCRIPTION
Bandage is a GUI program that allows users to interact with the assembly
graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and
others..
.SH OPTIONS
.SS Commands
.TP
<blank> Launch the Bandage GUI
.TP
load
Launch the Bandage GUI and load a graph file
.TP
info
Display information about a graph
.TP
image
Generate an image file of a graph
.TP
querypaths
Output graph paths for BLAST queries
.TP
reduce
Save a subgraph of a larger graph
.SS Options
.TP
\fB\-\-help\fR
View this help message
.TP
\fB\-\-helpall\fR
View all command line settings
.TP
\fB\-\-version\fR
View Bandage version number
.SS Settings
The following options configure the Bandage settings that are available in the Bandage GUI.
.TP
Colours can be specified using hex values, with or without an alpha channel, (e.g. #FFB6C1 or #7FD2B48C) or using standard colour names (e.g. red, yellowgreen or skyblue).
Note that hex colours will
either need to be enclosed in quotes (e.g. "#FFB6C1") or have the hash symbol escaped (e.g. \e#FFB6C1).
.PP
.B Graph scope
.PP
These settings control the graph scope. If the aroundnodes scope is used, then the \fB\-\-nodes\fR option must also be used. If the aroundblast scope is used, a BLAST query must be given with the \fB\-\-query\fR
option
.TP
\fB\-\-scope\fR <scope>
Graph scope, from one of the following options: entire, aroundnodes, aroundblast, depthrange (default: entire)
.TP
\fB\-\-nodes\fR <list>
A comma\-separated list of starting nodes for the aroundnodes scope (default: none)
.TP
\fB\-\-partial\fR
Use partial node name matching (default: exact node name matching)
.TP
\fB\-\-distance\fR <int>
The number of node steps away to draw for the aroundnodes and aroundblast scopes (0 to 100, default: 0)
.TP
\fB\-\-mindepth\fR <float>
The minimum allowed depth for the depthrange scope (0 to 1e+6, default: 10)
.TP
\fB\-\-maxdepth\fR <float>
The maximum allowed depth for the depthrange scope (0 to 1e+6, default: 100)
.TP
\fB\-\-double\fR
Draw graph in double mode (default: off)
.PP
.B Graph size
.TP
\fB\-\-nodelen\fR <float>
Node length per megabase (0 to 1e+6, default: auto)
.TP
\fB\-\-minnodlen\fR <float>
Minimum node length (1 to 100, default: 5)
.TP
\fB\-\-edgelen\fR <float>
Edge length (0.1 to 100, default: 5)
.TP
\fB\-\-edgewidth\fR <float>
Edge width (0.1 to 100, default: 1.5)
.TP
\fB\-\-doubsep\fR <float>
Double mode separation (0 to 100, default: 2)
.PP
.B Graph layout
.TP
\fB\-\-nodseglen\fR <float>
Node segment length (1 to 1000, default: 20)
.TP
\fB\-\-iter\fR <int>
Graph layout iterations (0 to 4, default: 2)
.TP
\fB\-\-linear\fR
Linear graph layout (default: off)
.PP
.B Graph appearance
.TP
\fB\-\-edgecol\fR <col>
Colour for edges (default: black)
.TP
\fB\-\-outcol\fR <col
Colour for node outlines (default: black)
.TP
\fB\-\-outline\fR <float>
Node outline thickness (0 to 100, default: 0)
.TP
\fB\-\-selcol\fR <col>
Colour for selections (default: blue)
.TP
\fB\-\-noaa\fR
Disable antialiasing (default: antialiasing on)
.TP
\fB\-\-singlearr\fR
Show node arrowheads in single mode (default: nodes are only displayed with arrowheads in double mode)
.PP
.B Text appearance
.TP
\fB\-\-textcol\fR <col>
Colour for label text (default: black)
.TP
\fB\-\-toutcol\fR <col>
Colour for text outline (default: white)
.TP
\fB\-\-toutline\fR <float>
Surround text with an outline with this thickness (0 to 10, default: 1.5)
.TP
\fB\-\-centre\fR
Node labels appear at the centre of the node (default: off, node labels appear over visible parts of nodes)
.PP
.B Node width
.PP
Node widths are determined using the following formula:
.IP
a*b*((c/d)^e\-1)+1
.IP
a = average node width
.IP
b = depth effect on width
.IP
c = node depth
.IP
d = mean depth
.IP
e = power of depth effect on width
.TP
\fB\-\-nodewidth\fR <float>
Average node width (0.5 to 1000, default: 5)
.TP
\fB\-\-depwidth\fR <float>
Depth effect on width (0 to 1, default: 0.5)
.TP
\fB\-\-deppower\fR <float>
Power of depth effect on width (0 to 1, default: 0.5)
.PP
.B Node labels
.TP
\fB\-\-names\fR
Label nodes with name (default: off)
.TP
\fB\-\-lengths\fR
Label nodes with length (default: off)
.TP
\fB\-\-depth\fR
Label nodes with depth (default: off)
.TP
\fB\-\-blasthits\fR
Label BLAST hits (default: off)
.TP
\fB\-\-fontsize\fR <int>
Font size for node labels (1 to 100, default: 12)
.PP
.B Node colours
.TP
\fB\-\-colour\fR <scheme>
Node colouring scheme, from one of the following options: random, uniform, depth, blastsolid, blastrainbow (default: random if \fB\-\-query\fR option not used, blastsolid if \fB\-\-query\fR
option used)
.PP
.B Random colour scheme
.PP
These settings only apply when the random colour scheme is used.
.TP
\fB\-\-ransatpos\fR <int>
Positive node saturation (0 to 255, default: 127)
.TP
\fB\-\-ransatneg\fR <int>
Negative node saturation (0 to 255, default: 127)
.TP
\fB\-\-ranligpos\fR <int>
Positive node lightness (0 to 255, default: 150)
.TP
\fB\-\-ranligneg\fR <int>
Negative node lightness (0 to 255, default: 90)
.TP
\fB\-\-ranopapos\fR <int>
Positive node opacity (0 to 255, default: 255)
.TP
\fB\-\-ranopaneg\fR <int>
Negative node opacity (0 to 255, default: 255)
.PP
.B Uniform colour scheme
.PP
These settings only apply when the uniform colour scheme is used.
.TP
\fB\-\-unicolpos\fR <col>
Positive node colour (default: firebrick)
.TP
\fB\-\-unicolneg\fR <col>
Negative node colour (default: maroon)
.TP
\fB\-\-unicolspe\fR <col>
Special node colour (default: green)
.PP
.B Depth colour scheme
.PP
These settings only apply when the depth colour scheme is used.
.TP
\fB\-\-depcollow\fR <col>
Colour for nodes with depth below the low depth value (default: black)
.TP
\fB\-\-depcolhi\fR <col>
Colour for nodes with depth above the high depth value (default: red)
.TP
\fB\-\-depvallow\fR <float>
Low depth value (0 to 1e+6, default: auto)
.TP
\fB\-\-depvalhi\fR <float>
High depth value (0 to 1e+6, default: auto)
.PP
.B BLAST search
.TP
\fB\-\-query\fR <fastafile>
A FASTA file of either nucleotide or protein sequences to be used as BLAST queries (default: none)
.TP
\fB\-\-blastp\fR <param>
Parameters to be used by blastn and tblastn when conducting a BLAST search in Bandage (default: none). Format BLAST parameters exactly as they would be used for blastn/tblastn on
the command line, and enclose them in quotes.
.TP
\fB\-\-alfilter\fR <int>
Alignment length filter for BLAST hits. Hits with shorter alignments will be excluded (1 to 1e+6, default: off)
.TP
\fB\-\-qcfilter\fR <float>
Query coverage filter for BLAST hits. Hits with less coverage will be excluded (0 to 100, default: off)
.TP
\fB\-\-ifilter\fR <float>
Identity filter for BLAST hits. Hits with less identity will be excluded (0 to 100, default: off)
.TP
\fB\-\-evfilter\fR <sci>
E\-value filter for BLAST hits. Hits with larger e\-values will be excluded (1e\-999 to 9.9e1, default: off)
.TP
\fB\-\-bsfilter\fR <float>
Bit score filter for BLAST hits. Hits with lower bit scores will be excluded (0 to 1e+6, default: off)
.PP
.B BLAST query paths
.PP
These settings control how Bandage searches for query paths after conducting a BLAST search.
.TP
\fB\-\-pathnodes\fR <int>
The number of allowed nodes in a BLAST query path (1 to 50, default: 6)
.TP
\fB\-\-minpatcov\fR <float>
Minimum fraction of a BLAST query which must be covered by a query path (0.3 to 1, default: 0.9)
.TP
\fB\-\-minhitcov\fR <float>
Minimum fraction of a BLAST query which must be covered by BLAST hits in a query path (0.3 to 1, default: 0.9)
.TP
\fB\-\-minmeanid\fR <float>
Minimum mean identity of BLAST hits in a query path (0 to 1, default: 0.5)
.TP
\fB\-\-maxevprod\fR <sci>
Maximum e\-value product for all BLAST hits in a query path (1e\-999 to 9.9e1, default: 1e\-10)
.TP
\fB\-\-minpatlen\fR <float>
Minimum allowed relative path length as compared to the query (0 to 10000, default: 0.95)
.TP
\fB\-\-maxpatlen\fR <float>
Maximum allowed relative path length as compared to the query (0 to 10000, default: 1.05)
.TP
\fB\-\-minlendis\fR <int>
Minimum allowed length discrepancy (in bases) between a BLAST query and its path in the graph (\fB\-1e\fR+6 to 1e+6, default: off)
.TP
\fB\-\-maxlendis\fR <int>
Maximum allowed length discrepancy (in bases) between a BLAST query and its path in the graph (\fB\-1e\fR+6 to 1e+6, default: off)
.SH SEE ALSO
Online Bandage help: https://github.com/rrwick/Bandage/wiki
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
debian/changelog
View file @ de4aacc5
......@@ -2,4 +2,4 @@ bandage (0.8.1-1) UNRELEASED; urgency=medium
* Initial release (Closes: #872622)
-- DMPT <debian-med-packaging@lists.alioth.debian.org> Tue, 15 Aug 2017 16:57:55 +0200
-- Andreas Tille <tille@debian.org> Sun, 26 Aug 2018 21:01:25 +0200
debian/control
View file @ de4aacc5
Source: bandage
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Cédric Lood <cedric.lood@kuleuven.be>
Uploaders: Cédric Lood <cedric.lood@kuleuven.be>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
qtbase5-dev,
libqt5svg5-dev
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bandage.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/bandage.git
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/bandage
Vcs-Git: https://salsa.debian.org/med-team/bandage.git
Homepage: https://rrwick.github.io/Bandage
Package: bandage
......
debian/createmanpages 0 → 100755
View file @ de4aacc5
#!/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: *//'`
PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//'`
AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
can be used for any other usage of the program.
"
# If program name is different from package name or title should be
# different from package short description change this here
progname=Bandage
help2man --no-info --no-discard-stderr --help-option=" --helpall" \
--name="$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/patches/fix_target_path.patch 0 → 100644
View file @ de4aacc5
Author: Andreas Tille <tille@debian.org>
Last-Update: Sun, 26 Aug 2018 19:57:42 +0200
Description: Install binary to /usr/bin
--- a/Bandage.pro
+++ b/Bandage.pro
@@ -24,7 +24,7 @@ TEMPLATE = app
CONFIG += c++11
-target.path += /usr/local/bin
+target.path += /usr/bin
INSTALLS += target
INCLUDEPATH += ui
debian/patches/series
View file @ de4aacc5
fix_include_vars_makefile.patch
fix_target_path.patch
debian/rules
View file @ de4aacc5
......@@ -16,8 +16,14 @@ include /usr/share/dpkg/default.mk
# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
export QT_SELECT = qt5
%:
dh $@
#get-orig-source:
# . debian/get-orig-source
override_dh_auto_configure:
# see https://lists.debian.org/debian-mentors/2018/08/msg00206.html
# --> thus move the other .pro file that confuses qmake out of the way
mv BandageTests.pro BandageTests.pro_do_not_use
dh_auto_configure
# restore original status of source dir
mv BandageTests.pro_do_not_use BandageTests.pro