git config --global http.postBuffer 5242880000
git clone https://github.com/zhangrengang/OGAP
cd OGAP
# install
conda env create -f OGAP.yaml
conda activate OGAP
#python setup.py install
# start
cd test
python ../OGAP.py Arabidopsis_thaliana-mt.gb -mt -o mt_out
python ../OGAP.py Arabidopsis_thaliana-mt.fa -mt -o mt_out -sp Arabidopsis_thaliana
python ../OGAP.py Arabidopsis_thaliana-pt.gb -pt -o pt_out
python ../OGAP.py Arabidopsis_thaliana-mt.gb -mt -pt -o mt_out
Dependencies:
pip2 install biopython<=1.76
pip2 install networkx<2.0
pip2 install lazy-property
hmmsearch 3.1x or 3.2x: compatible with HMMER3/f database format
exonerate for coding genes annotation
augustus for coding genes annotation
tRNAscan-SE for tRNA genes annotation
blat for rRNA genes annotation
tbl2asn output sqn file for submitting to GenBank
asn2gb output genbank file
without -taxon
option to automatically get taxon from organism
-trn_struct
option to plot tRNA secondary structure
-draw_map
option to draw Genome Map
-compare_map
option to draw Genome Map together with the raw genbank record
-repeat
option to annotate repeat region
to compare multiple annotations (Comparative.py)
to build custom database (Database.py)
OGAP:
git clone https://github.com/zhangrengang/OGAP
cd OGAP/test
python ../OGAP.py Arabidopsis_thaliana-mt.gb -mt -o mt_out
By default, organism name will be extract from the genbank file (ORGANISM) and database will be selected by taxonomy mapping from organism, automatically.
python ../OGAP.py Arabidopsis_thaliana-mt.fa -mt -o mt_out -sp Arabidopsis_thaliana
By default, database will be selected by taxonomy mapping from organism (-sp
), automatically.
-taxon
)python ../OGAP.py Arabidopsis_thaliana-mt.fa -mt -o mt_out -sp Arabidopsis_thaliana -taxon rosids
python ../OGAP.py Arabidopsis_thaliana-mt.fa -mt -o mt_out -sp Arabidopsis_thaliana -taxon rosids malvids
-pt
modepython ../OGAP.py Arabidopsis_thaliana-pt.gb -pt -o pt_out
python ../OGAP.py Arabidopsis_thaliana-mt.gb -mt -pt -o mt_out
for sp in Arabidopsis_thaliana Vitis_vinifera Oryza_sativa Salix_suchowensis Citrus_sinensis
do
python ../OGAP.py genbank/$sp.gb -mt -prefix $sp -outdir re_anno &> $sp.log
done
python ../lib/Comparative.py summary re_anno/
python ../lib/Comparative.py phylo re_anno/
python ../lib/Comparative.py kaks re_anno/