Commit 027e8425 authored by Andreas Tille's avatar Andreas Tille

New upstream version 1.1

parent 0951c5a6
repo: 0fdb21ec3cf53e710d679fbd7768f91510570ae7
node: edea23ce7c21765cbd9ff601e1f91614241eae81
branch: default
tag: 1.1
syntax: glob
.hgignore
*.pyc
*.DS_Store
*.log
examples/test/
pyphlan = https://bitbucket.org/nsegata/pyphlan
export2graphlan = https://bitbucket.org/cibiocm/export2graphlan
b2e0ba66718673ea28cb217c8e5dcd8e578fd033 export2graphlan
eae40ebc0030c7179baed999c74de412ba696598 pyphlan
0000000000000000000000000000000000000000 v0.8
0000000000000000000000000000000000000000 v0.8
0fdb21ec3cf53e710d679fbd7768f91510570ae7 v0.8
ba9c6f680022333b5b1bf0652748ab2db29e888a 0.9
eaa3d2e05d74912da0f013bbfbb199764b180f05 0.9.5
64570f7d4ae33f46ddd360101c13555396a0cab1 0.9.6
7d483b7d34ccadb30f5c56f82b7aab19a820d1d6 1.0
Notes on how this package can be tested.
────────────────────────────────────────
GraPhlAn comes with a set of examples which can be found in a
subdirectory here. You can use the shell scripts inside the
subdirectories for testing but you need to copy the files to
some place werte you have write permissions and gunzip the
compressed data files.
Alternatively you can run the script run-unit-test in this
directory which runs all available examples as tests.
Some tests are requiring
https://bitbucket.org/CibioCM/export2graphlan/
which would need to be packaged (see
https://lists.debian.org/debian-med/2016/06/msg00110.html
)
graphlan (1.1-2) unstable; urgency=medium
* Fix watch file
* debhelper 10
-- Andreas Tille <tille@debian.org> Mon, 09 Jan 2017 17:13:45 +0100
graphlan (1.1-1) unstable; urgency=medium
* Initial release (Closes: #826005)
-- Andreas Tille <tille@debian.org> Wed, 01 Jun 2016 13:16:34 +0200
Source: graphlan
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
python-all,
dh-python
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/graphlan/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/graphlan/trunk/
Homepage: https://bitbucket.org/nsegata/graphlan/wiki/Home
Package: graphlan
Architecture: all
Depends: ${python:Depends},
${misc:Depends},
python-biopython,
python-numpy,
python-matplotlib
Description: circular representations of taxonomic and phylogenetic trees
GraPhlAn is a software tool for producing high-quality circular
representations of taxonomic and phylogenetic trees. It focuses on
concise, integrative, informative, and publication-ready representations
of phylogenetically- and taxonomically-driven investigation.
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: GraPhlAn
Upstream-Contact: Nicola Segata <nicola.segata@unitn.it>
Source: https://bitbucket.org/nsegata/graphlan/src
Files: *
Copyright: 2012-2016 Nicola Segata and Curtis Huttenhower
License: expat
Files: debian/*
Copyright: 2016 Andreas Tille <tille@debian.org>
License: expat
License: expat
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
.
The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.
.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EV ENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR TH E USE OR OTHER DEALINGS IN THE SOFTWARE.
debian/README.test
debian/tests/run-unit-test
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH GRAPHLAN "1" "June 2016" "graphlan 1.1" "User Commands"
.SH NAME
graphlan \- circular representations of taxonomic and phylogenetic trees
.SH SYNOPSIS
.B graphlan
[\-h] [\-\-format ['output_image_format']] [\-\-warnings WARNINGS]
[\-\-positions POSITIONS] [\-\-dpi image_dpi] [\-\-size image_size]
[\-\-pad pad_in] [\-\-external_legends] [\-v]
input_tree output_image
.SH DESCRIPTION
GraPhlAn is a software tool for producing high-quality circular
representations of taxonomic and phylogenetic trees. It focuses on
concise, integrative, informative, and publication-ready representations
of phylogenetically- and taxonomically-driven investigation.
.SH OPTIONS
.SS "positional arguments:"
.TP
input_tree
the input tree in PhyloXML format
.TP
output_image
the output image, the format is guessed from the
extension unless \fB\-\-format\fR is given. Available file
formats are: png, pdf, ps, eps, svg
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-format\fR ['output_image_format']
set the format of the output image (default none
meaning that the format is guessed from the output
file extension)
.TP
\fB\-\-warnings\fR WARNINGS
set whether warning messages should be reported or not
(default 1)
.TP
\fB\-\-positions\fR POSITIONS
set whether the absolute position of the points should
be reported on the standard output. The two
cohordinates are r and theta
.TP
\fB\-\-dpi\fR image_dpi
the dpi of the output image for non vectorial formats
.TP
\fB\-\-size\fR image_size
the size of the output image (in inches, default 7.0)
.TP
\fB\-\-pad\fR pad_in
the distance between the most external graphical
element and the border of the image
.TP
\fB\-\-external_legends\fR
specify whether the two external legends should be put
in separate file or keep them along with the image
(default behavior)
.TP
\fB\-v\fR, \fB\-\-version\fR
Prints the current GraPhlAn version and exit
.SH AUTHOR
The software was written by Nicola Segata <nsegata@hsph.harvard.edu>
.P
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH GRAPHLAN_ANNOTATE "1" "June 2016" "graphlan_annotate 1.1" "User Commands"
.SH NAME
graphlan_annotate \- GraPhlAn annotate module
.SH SYNOPSIS
.B graphlan_annotate
[\-h] [\-\-annot annotation_file] [\-v]
input_tree [output_tree]
.SH DESCRIPTION
GraPhlAn is a software tool for producing high-quality circular
representations of taxonomic and phylogenetic trees. It focuses on
concise, integrative, informative, and publication-ready representations
of phylogenetically- and taxonomically-driven investigation.
.P
graphlan_annotate is the annotate module of graphlan(1).
.SH OPTIONS
.SS "positional arguments:"
.TP
input_tree
the input tree in Newick, Nexus, PhyloXML or plain
text format
.TP
output_tree
the output tree in PhyloXML format containing the
newly added annotations. If not specified, the input
tree file will be overwritten
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-annot\fR annotation_file
specify the annotation file
.TP
\fB\-v\fR, \fB\-\-version\fR
Prints the current GraPhlAn version and exit
.SH SEE ALSO
graphlan(1)
.SH AUTHOR
The software was written by Nicola Segata <nsegata@hsph.harvard.edu>
.P
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
graphlan*.py usr/share/graphlan
src usr/share/graphlan
usr/share/graphlan/graphlan.py usr/bin/graphlan
usr/share/graphlan/graphlan_annotate.py usr/bin/graphlan_annotate
#!/usr/bin/make -f
# DH_VERBOSE := 1
export LC_ALL=C.UTF-8
%:
dh $@ --with python2
override_dh_installexamples:
dh_installexamples
for sh in `find debian/*/usr/share/doc/*/examples -type f -name "*.sh"` ; do \
sed -i -e 's/graphlan_annotate.py/graphlan_annotate/g' -e 's/graphlan.py/graphlan/g' $${sh} ; \
if ! head -n1 $${sh} | grep -q '/bin/sh' ; then \
sed -i '1i #!/bin/sh' $${sh} ; \
fi ; \
done
Tests: run-unit-test
Depends: @, r-cran-gsl, r-cran-randomfields
Restrictions: allow-stderr
#!/bin/sh -e
pkg=graphlan
if [ "$ADTTMP" = "" ] ; then
ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
cd $ADTTMP
cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
find . -name "*.gz" -exec gunzip \{\} \;
for testdir in `find . -mindepth 1 -maxdepth 1 -type d` ; do
cd $testdir
for tscript in `ls *.sh | sort` ; do
if grep -q export2graphlan $tscript ; then
echo "Test script $testdir/$tscript requires export2graphlan which is not available."
else
echo "Running test script $testdir/$tscript ."
sh $tscript
fi
done
cd ..
done
rm -rf $ADTTMP/*
version=4
https://bitbucket.org/nsegata/graphlan/downloads?tab=tags .*/(\d\S*)\.tar\.gz
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#!/bin/sh
cp annot.txt annot3.txt
# De Filippo
for l in `cat genomes.all.txt | grep g__Prevotella | cut -f 1 | sed -n '0~4p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Xylanibacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Treponema | cut -f 1 | sed -n '0~4p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Butyrivibrio | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
# Yatsunenko
for l in `cat genomes.all.txt | grep s__Streptococcus_alactolyticus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Clostridium.s__leptum | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep s__Clostridium_orbiscindens | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep s__Clostridium_innocuum | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Lactobacillus.s__ruminis | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Eubacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Dialister | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Oscillospira | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
# Clemente
for l in `cat genomes.all.txt | grep g__Helicobacter | cut -f 1 | sed -n '0~6p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Phascolarctobacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Paraprevotella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Anaeroplasma | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Bulleidia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Gemella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Coprococcus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
#Martinez
for l in `cat genomes.all.txt | grep g__Weissella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Slackia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Gemella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Streptococcus | cut -f 1 | sed -n '0~14p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Gordonibacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Odoribacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
# Obregon
for l in `cat genomes.all.txt | grep g__Succinivibrio | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Catenibacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Dorea | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Blautia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Bacteroides | cut -f 1 | sed -n '0~14p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Faecalibacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Ruminococcus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
graphlan_annotate.py DisMic.xml DisMic.annot.xml --annot annot3.txt
graphlan.py DisMic.annot.xml DisMic.png --dpi 200 --size 15 --pad 0.6
graphlan.py DisMic.annot.xml DisMic.svg --dpi 200 --size 15 --pad 0.6
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#!/bin/sh
graphlan_annotate.py hmptree.xml hmptree.annot.xml --annot annot.txt
graphlan.py hmptree.annot.xml hmptree.png --dpi 150 --size 14
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#!/bin/sh
graphlan_annotate.py hmptree.xml hmptree.annot.xml --annot annot.txt
graphlan.py hmptree.annot.xml hmptree.png --dpi 150 --size 14
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#!/bin/sh
graphlan_annotate.py IBDgeo.txt IBDgeo.annot.xml --annot annotation.txt
graphlan.py IBDgeo.annot.xml IBDgeo.png --dpi 150
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#!/bin/sh
graphlan_annotate.py ppa_tol.xml ppa_tol.annot.xml --annot annot.txt
graphlan.py ppa_tol.annot.xml ppa_tol.png --dpi 200 --size 15 --pad 0.6
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#!/bin/sh
graphlan_annotate.py archaea.txt archaea.annot.xml --annot annot.txt
graphlan.py archaea.annot.xml archaea.png --dpi 150 --pad 0
clade_separation 0.5
branch_thickness 1.5
branch_bracket_depth 0.8
branch_bracket_width 0.25
clade_marker_size 40
clade_marker_edge_color #555555
clade_marker_edge_width 1.2
Banthracis clade_marker_color b
Banthracis clade_marker_size 80
Saureus clade_marker_color r
Saureus clade_marker_size 125
Bacillus clade_marker_color b
Bacillus clade_marker_size 120
Bacillus clade_marker_shape h
Pcurdlanolyticus clade_marker_color #20DD20
Plarvae clade_marker_color #008000
Pmucilaginosus clade_marker_color #057005
Ppolymyxa clade_marker_color #009020
Pvortex clade_marker_color #00AA00
Bacillaceae clade_marker_shape *
Bacillaceae clade_marker_size 130
Bacillaceae clade_marker_color b
Listeriaceae clade_marker_shape *
Listeriaceae clade_marker_size 130
Paenibacillaceae clade_marker_shape *
Paenibacillaceae clade_marker_size 130
Paenibacillaceae clade_marker_color g
Staphylococcaceae clade_marker_shape *
Staphylococcaceae clade_marker_size 130
Staphylococcaceae clade_marker_color r
Batrophaeus clade_marker_size 12
Bcellulosilyticus clade_marker_size 8
Bcereus clade_marker_size 3
Scarnosus clade_marker_size 75
Plarvae clade_marker_size 89
Bpumilus clade_marker_size 50
Bsubtilis clade_marker_size 65
Bthuringiensis clade_marker_size 10
Cthermarum clade_marker_size 15
Bmegaterium clade_marker_size 12
Lfusiformis clade_marker_size 174
Oiheyensis clade_marker_size 95
Scapitis clade_marker_size 36
Shaemolyticus clade_marker_size 64
Ppolymyxa clade_marker_size 20
Pvortex clade_marker_size 19
Swarneri clade_marker_size 33
Spseudintermedius clade_marker_size 19
Bacillus annotation Bacillus
Bacillaceae annotation Bacillaceae
Bacillus annotation_background_color b
Bacillaceae annotation_background_color b
Paenibacillaceae annotation Paenibacillaceae
Paenibacillaceae annotation_background_color g
Staphylococcus annotation Staphylococcus
Staphylococcus annotation_background_color r
Saureus annotation S. aureus
Saureus annotation_background_color r
Paenibacillus annotation Paenibacillus
Paenibacillus annotation_background_color g
Staphylococcaceae annotation Staphylococcaceae
Staphylococcaceae annotation_background_color r
Brevibacillus annotation Brevibacillus
Brevibacillus annotation_background_color g
Bbrevis annotation a:Brevibacillus brevis
Bbrevis annotation_background_color g
Blaterosporus annotation b:Brevibacillus laterosporus
Blaterosporus annotation_background_color g
Banthracis annotation Bacillus anthracis
Banthracis annotation_background_color b
Bsubtilis annotation Bacillus subtilis
Bsubtilis annotation_background_color b
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Bacillaceae.Anoxybacillus.Aflavithermus
Bacillaceae.Bacillus.Bamyloliquefaciens
Bacillaceae.Bacillus.Banthracis
Bacillaceae.Bacillus.Batrophaeus
Bacillaceae.Bacillus.Bcellulosilyticus
Bacillaceae.Bacillus.Bcereus
Bacillaceae.Bacillus.Bclausii
Bacillaceae.Bacillus.Bcoagulans
Bacillaceae.Bacillus.Bcoahuilensis
Bacillaceae.Bacillus.Bhalodurans
Bacillaceae.Bacillus.Blicheniformis
Bacillaceae.Bacillus.Bmegaterium
Bacillaceae.Bacillus.Bmycoides
Bacillaceae.Bacillus.Bpseudofirmus
Bacillaceae.Bacillus.Bpseudomycoides
Bacillaceae.Bacillus.Bpumilus
Bacillaceae.Bacillus.Bselenitireducens
Bacillaceae.Bacillus.Bsubtilis
Bacillaceae.Bacillus.Bthuringiensis
Bacillaceae.Bacillus.Bweihenstephanensis
Bacillaceae.Caldalkalibacillus.Cthermarum
Bacillaceae.Geobacillus.Gkaustophilus
Bacillaceae.Geobacillus.Gthermodenitrificans
Bacillaceae.Geobacillus.Gthermoglucosidasius
Bacillaceae.Lysinibacillus.Lfusiformis
Bacillaceae.Lysinibacillus.Lsphaericus
Bacillaceae.Oceanobacillus.Oiheyensis
Listeriaceae.Listeria.Lgrayi
Listeriaceae.Listeria.Linnocua
Listeriaceae.Listeria.Lmonocytogenes
Listeriaceae.Listeria.Lseeligeri
Listeriaceae.Listeria.Lwelshimeri
Paenibacillaceae.Brevibacillus.Bbrevis
Paenibacillaceae.Brevibacillus.Blaterosporus
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus
Paenibacillaceae.Paenibacillus.Plarvae
Paenibacillaceae.Paenibacillus.Pmucilaginosus
Paenibacillaceae.Paenibacillus.Ppolymyxa
Paenibacillaceae.Paenibacillus.Pvortex
Staphylococcaceae.Macrococcus.Mcaseolyticus
Staphylococcaceae.Staphylococcus.Saureus
Staphylococcaceae.Staphylococcus.Scapitis
Staphylococcaceae.Staphylococcus.Scaprae
Staphylococcaceae.Staphylococcus.Scarnosus
Staphylococcaceae.Staphylococcus.Sepidermidis
Staphylococcaceae.Staphylococcus.Shaemolyticus
Staphylococcaceae.Staphylococcus.Shominis
Staphylococcaceae.Staphylococcus.Slugdunensis
Staphylococcaceae.Staphylococcus.Spseudintermedius
Staphylococcaceae.Staphylococcus.Ssaprophyticus
Staphylococcaceae.Staphylococcus.Swarneri
graphlan.py guide.txt step_0.png --dpi 300 --size 3.5
graphlan.py guide.txt step_0.svg --dpi 300 --size 3.5
graphlan_annotate.py --annot annot_0.txt guide.txt guide_1.xml
graphlan.py guide_1.xml step_1.png --dpi 300 --size 3.5
graphlan.py guide_1.xml step_1.svg --dpi 300 --size 3.5
graphlan_annotate.py --annot annot_1.txt guide_1.xml guide_2.xml
graphlan.py guide_2.xml step_2.png --dpi 300 --size 3.5
graphlan.py guide_2.xml step_2.svg --dpi 300 --size 3.5
graphlan_annotate.py --annot annot_2.txt guide_2.xml guide_3.xml
graphlan.py guide_3.xml step_3.png --dpi 300 --size 3.5
graphlan.py guide_3.xml step_3.svg --dpi 300 --size 3.5
graphlan_annotate.py --annot annot_3.txt guide_3.xml guide_4.xml
graphlan.py guide_4.xml step_4.png --dpi 300 --size 3.5 --pad 0.0
graphlan.py guide_4.xml step_4.svg --dpi 300 --size 3.5 --pad 0.0
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#!/bin/sh
graphlan_annotate.py gut_microbiome.txt gut_microbiome.annot.xml --annot annot.txt
graphlan.py gut_microbiome.annot.xml gut_microbiome.png --dpi 300 --size 4.5 --pad 0
# !/bin/bash
########################################################################################################################
# The following lines of code contains all the steps for downloading the HMP and MetaHIT data, process it through #
# MetaPhlAn2, merging the MetaPhlAn2 results into a single dataset, perform some string manipulation, process the data #
# using LEfSe for biomarkers discovery, exploit the export2graphlan framework for generating the tree and the #
# annotation file for GraPhlAn, and finally draw the image using GraPhlAn. #
# For time reasons, we provide the two intermediate files: the clean merge of the two datasets (HMP & MetaHIT) and the #
# results of LEfSE. #
# If the user wants to test the complete pipeline, it is enough to uncommet all the commented part. #
########################################################################################################################
# # remove the generated files, if any
# echo "Removing files"
# rm -f merge.txt new-stool/* merge-good.txt merge-good-1.txt merge-good-2.txt merge-good-3.txt merge-very-good.txt \
# merge-very-good.txt.in merge-very-good.txt.out tree.txt annot.txt outtree.txt outimg.png
# # set MetaPhlAn2 directory
# mpa_dir=`$HOME/metaphlan2`
# # download samples
# echo "Downloading HMP stool samples"
# mkdir new-stool
# cd new-stool/
# for i in SRS011239 SRS013215 SRS013476 SRS014459 SRS015065 SRS056259 SRS058770 SRS062427 SRS063985 SRS015854 SRS016203 \
# SRS016335 SRS017307 SRS017701 SRS018656 SRS019161 SRS019968 SRS020233 SRS020328 SRS022609 SRS023583 SRS024265 \
# SRS047044 SRS052697 SRS053214 SRS015190 SRS015217 SRS015578 SRS015663 SRS016056 SRS016989 SRS017191 SRS017433 \
# SRS018351 SRS018427 SRS018984 SRS019582 SRS019601 SRS022071 SRS022137 SRS024009 SRS024132 SRS024549 SRS024625 \
# SRS043001 SRS045004 SRS045713 SRS050422 SRS050925 SRS051031 SRS011405 SRS011529 SRS011586 SRS012902 SRS014923 \
# SRS055982 SRS011084 SRS011134 SRS011452 SRS013951 SRS014613 SRS014979 SRS054956 SRS057717 SRS058723 SRS064557 \
# SRS064645 SRS065504 SRS015264 SRS015782 SRS015960 SRS016495 SRS016517 SRS017103 SRS018313 SRS018575 SRS019267 \
# SRS019787 SRS019910 SRS020869 SRS021484 SRS023176 SRS023526 SRS023971 SRS024331 SRS024435 SRS048870 SRS049900 \
# SRS049959 SRS049995 SRS050299 SRS050752 SRS052027 SRS011302 SRS012273 SRS013158 SRS014313 SRS015133 SRS053335 \
# SRS054590 SRS063040 SRS077730 SRS078176 SRS015369 SRS015890 SRS016018 SRS016095 SRS016753 SRS016954 SRS017521 \
# SRS017821 SRS018133 SRS019030 SRS019685 SRS022713 SRS023829 SRS024388 SRS042628 SRS047014 SRS048164 SRS049712 \
# SRS051882 SRS011061 SRS011271 SRS013521 SRS013687 SRS013800 SRS014235 SRS014287 SRS014683 SRS053398 SRS056519 \
# SRS057478 SRS064276 SRS075398 SRS015431 SRS015794 SRS016267 SRS016585 SRS017247 SRS018817 SRS019068 SRS019381 \
# SRS019397 SRS021948 SRS022524 SRS023346 SRS023914 SRS024075 SRS042284 SRS043411 SRS043701 SRS045645 SRS049164; do
# wget ftp://public-ftp.hmpdacc.org/Illumina/stool/${i}.tar.bz2 # download
# tar jxf -d ${i}.tar.bz2 # decompress
# cat ${i}/* > ${i}.fastq
# metaphlan2.py ${i}.fastq --mpa_pkl ${mpa_dir}/db_v20/mpa_v20_m200.pkl --bowtie2db ${mpa_dir}/db_v20/mpa_v20_m200 \
# --input_type fastq > ${i}.profile
# done
# echo "Downloading MetaHIT healthy stool samples"
# for i in `cat ../metahit.txt`; do
# s=`echo ${i} | cut -f1`
# u=`echo ${i} | cut -f2`
# for j in `echo ${u} | tr ';' '\n'`; do
# f=`echo ${j} | cut -f6 -d'/'`
# ff=`echo ${f} | cut -f1-2 -d'.'`
# wget ftp://${j} # download
# gunzip ${f} # decompress
# cat ${ff} >> ${s}.fastq # cat forward and reverse
# done
# metaphlan2.py ${s}.fastq --mpa_pkl ${mpa_dir}/db_v20/mpa_v20_m200.pkl --bowtie2db ${mpa_dir}/db_v20/mpa_v20_m200 \
# --input_type fastq > ${s}.profile
# done
# cd ../
# # discard taxon rows in .profile files
# echo "Removing \"t__\" from taxonomy"
# for i in `ls new-stool/`; do
# file=new-stool/${i}
# grep -v t__ $file > $file.clean
# done
# rm -f new-stool/*.profile
# # merge tables
# echo "Merging tables"
# merge_metaphlan_tables.py new-stool/* > merge.txt
# # fix taxonomy
# echo "Cleaning taxonomy"
# sed 's/.__//g' merge.txt > merge-good.txt
# # put the dataset information (e.g., HMP or MetaHIT)
# # change "ID" with "dataset"
# sed 's/ID/dataset/' merge-good.txt > merge-good-1.txt
# # all "MH00*" must become "MetaHIT"
# sed 's/MH00[0-9]*.profile/MetaHIT/g' merge-good-1.txt > merge-good-2.txt
# # all "V1.CD-* must become "MetaHIT"
# sed 's/V1.[A-Z]*-[0-9]*.profile/MetaHIT/g' merge-good-2.txt > merge-good-3.txt
# # all "SRS*" must become "HMP"
# sed 's/SRS[0-9]*.profile/HMP/g' merge-good-3.txt > merge-very-good.txt
# # execute LEfSe
# echo "Running LEfSe"
# format_input.py merge-very-good.txt merge-very-good.txt.in -c 1 -o 1000000
# run_lefse.py -l 3.0 merge-very-good.txt.in merge-very-good.txt.out
# convert it!
echo "Converting to GraPhlAn"
export2graphlan.py -i merge-very-good.txt -o merge-very-good.txt.out -t tree.txt -a annot.txt \
--title "MetaHIT vs. HMP (MetaPhlAn 2)" --max_clade_size 250 --min_clade_size 40 --annotations 5 \
--external_annotations 6,7 --abundance_threshold 40.5 --fname_row 0 --ftop 200 --annotation_legend_font_size 11
echo "Running Graphlan"
graphlan_annotate.py --annot annot.txt tree.txt outtree.txt # attach annotation to the tree
graphlan.py --dpi 300 --size 7.0 outtree.txt aaa.svg # generate the beautiful image
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# !/bin/bash
########################################################################################################################
# The following lines of code contains all the steps for downloading the HMP and MetaHIT data, process it through #
# MetaPhlAn2, perform the functional analysis using HUMAnN, merging the functional profiles by means of an ad-hoc #
# python script provided inside the hmp_metahit_functional folder, process the merged dataset with LEfSe for #
# biomarkers discovery, exploit the export2graphlan framework for generating the tree and the annotation file for #
# GraPhlAn, and finally draw the image using GraPhlAn. #
# For time reasons, we provide the two intermediate files: the merge of the two datasets (HMP & MetaHIT) and the #
# results of LEfSE. #
# If the user wants to test the complete pipeline, it is enough to uncommet all the commented part. #
########################################################################################################################
# # remove the generated files, if any
# echo "Removing files"
# rm -f merge.txt stool/* merge-good.txt merge-good-1.txt merge-good-2.txt merge-good-3.txt merge.txt merge.txt.in \
# merge.txt.out tree.txt annot.txt outtree.txt outimg.png