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View Code? Open in Web Editor NEWThis program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
License: GNU General Public License v3.0
This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
License: GNU General Public License v3.0
Hi,
Thank you for creating this nice tool.
It seems, I have an bug in my annotation.tsv output with bacant.
Below is how my input fasta looks like:
$ grep '>' filename.fasta
>Ctg1_len_5201677_depth_1.00x_circ
>Ctg2_len_135212_depth_2.08x_circ
>Ctg3_len_67445_depth_4.02x_circ
The annotation.tsv appends a number in the sequence name:
egrep 'circ1|circ2' annotation.tsv
Ctg1_len_5201677_depth_1.00x_circ2 resistance gene 939 1799 . - . locus_tag=Ctg1_len_5201677_depth_1.00x_circ2;gene=blaTEM-116;db_xref=ResDB;Note=BETA-LACTAM
Ctg1_len_5201677_depth_1.00x_circ2 resistance CDS 939 1799 . - . locus_tag=Ctg1_len_5201677_depth_1.00x_circ2;CDS=blaTEM-116;db_xref=ResDB;Note=BETA-LACTAM
Ctg1_len_5201677_depth_1.00x_circ1 resistance gene 613 933 . - . locus_tag=Ctg1_len_5201677_depth_1.00x_circ1;gene=ble_Tn5;db_xref=ResDB;Note=BLEOMYCIN
Ctg1_len_5201677_depth_1.00x_circ1 resistance CDS 613 933 . - . locus_tag=Ctg1_len_5201677_depth_1.00x_circ1;CDS=ble_Tn5;db_xref=ResDB;Note=BLEOMYCIN
Ctg1_len_5201677_depth_1.00x_circ1 resistance gene 954 1748 . - . locus_tag=Ctg1_len_5201677_depth_1.00x_circ1;gene=aph(3')-IIa;db_xref=ResDB;Note=KANAMYCIN
Ctg1_len_5201677_depth_1.00x_circ1 resistance CDS 954 1748 . - . locus_tag=Ctg1_len_5201677_depth_1.00x_circ1;CDS=aph(3')-IIa;db_xref=ResDB;Note=KANAMYCIN
Not all the gene annotations are like this but a few of them are as above. Any help appreciated!
Dear developer,
Thanks for your such good job.
My issue is that "FileNotFoundError: [Errno 2] No such file or directory: 'Bacant_out/annotation.gb'" occurenced and command line is
bacant -n ISO_1051.fna -o Bacant_out/
and output:
-rw-r--r-- 1 yu husn 150 Jun 1 21:27 AMR.possible.xls
-rw-r--r-- 1 yu husn 150 Jun 1 21:27 AMR.xls
-rw-r--r-- 1 yu husn 603 Jun 1 21:27 gb_location.txt
drwxr-xr-x 2 yu husn 4.0K Jun 1 21:27 multi_contig
-rw-r--r-- 1 yu husn 2.9M Jun 1 21:27 nucleotide.fasta
-rw-r--r-- 1 yu husn 20 Jun 1 21:27 nucleotide.integrons
-rw-r--r-- 1 yu husn 58 Jun 1 21:27 replicon.tsv
drwxr-xr-x 50 yu husn 4.0K Jun 1 21:27 Results_Integron_Finder_nucleotide
-rw-r--r-- 1 yu husn 7 Jun 1 21:27 seqLen.txt
-rw-r--r-- 1 yu husn 5 Jun 1 21:27 tmp.fasta
-rw-r--r-- 1 yu husn 162 Jun 1 21:27 transposon.filter.xls
-rw-r--r-- 1 yu husn 162 Jun 1 21:27 transposon.possible.xls
but the results except header line without anything.
and log:
Analysing file /share/disk6/yutao/test/ISO_1051.fna at 2021-06-01 21:27:27
replicon search done
AMR done
transposon done
integron_finder done
Traceback (most recent call last):
File "/home/yu/.local/bin/bacant", line 8, in <module>
sys.exit(run())
File "/home/yu/.local/lib/python3.7/site-packages/BacAnt/bacant.py", line 1194, in run
merge_genbank(resultdir)
File "/home/yu/.local/lib/python3.7/site-packages/BacAnt/bacant.py", line 1011, in merge_genbank
for rec in SeqIO.parse(annotation_file,'genbank'):
File "/home/yu/.local/lib/python3.7/site-packages/Bio/GenBank/Scanner.py", line 514, in parse_records
with as_handle(handle, "rU") as handle:
File "/home/miniconda2/envs/denovo/lib/python3.7/contextlib.py", line 112, in __enter__
return next(self.gen)
File "/home/yu/.local/lib/python3.7/site-packages/Bio/File.py", line 120, in as_handle
with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: 'Bacant_out/annotation.gb'
Looking forward your reply
Hi @xthua ,
Sorry to bother again. After the bacant update to v3.3.4, I get the integron_finder error.
I do not see the annotation.tsv file in the results folder either. This was not a problem in v3.3.3.
I have create a new environment with bacant v3.3.4, but with no success.
$ conda create -n bacant2
$ conda activate bacant2
$ conda install -c bacant -c conda-forge -c bioconda bacant
$ time bacant -n filename.fasta -o filename_bacant_out
Analysing file /home/user/filename.fasta at 2022-09-02 12:10:32
replicon search done
integron_finder error
AMR done
transposon done
All Done at 2022-09-02 12:10:59
may I know if I am missing something.
hi,I have tested bacant with genomic assembly drafts, however there w no html files created. Would you like to help me with this issue?
Thanks a lot.
The tool developed by the author is very good, but the software has not been updated for a long time, and the database is also the same. Could the author provide some scripts for building the database? For example, I can only find the corresponding web version for the data of transposon and integron at present
Hi,
Thank you for developping this tool. It is really great to be able to annotate several elements in one command line. After running Bacant v3.4.0 on some genomes I have some comments and questions:
Thank you
I would like to understand how the output results in transposon.possible.tsv are defined. What criteria are used to determine 'all possible transposon elements'?
Code used:
$ bacant --indir /data/users/kxytry/infile -o outdir
Error prompt
Traceback (most recent call last):
File "/data/users/kxy/miniconda3/envs/bacant/bin/bacant", line 33, in
sys.exit(load_entry_point('BacAnt==3.3.2', 'console_scripts', 'bacant')())
File "/data/users/kxy/miniconda3/envs/bacant/lib/python3.7/site-packages/BacAnt-3.3.2-py3.7.egg/BacAnt/bacant.py", line 1135, in run
process_dir(blastn_path,indir,resultdir)
File "/data/users/kxy/miniconda3/envs/bacant/lib/python3.7/site-packages/BacAnt-3.3.2-py3.7.egg/BacAnt/bacant.py", line 881, in process_dir
ident0 = float(ident0)
ValueError: could not convert string to float: '90,90,90'
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