Number appended after sequence name in annotation.tsv file

[ramadatta]

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!

[xthua]

Hi, Prakki: please send me your fasta file and the bacant version you used. Thank you very much! Best wishes, Xiaoting

-----原始邮件----- 发件人:"Prakki Rama" ***@***.***> 发送时间:2022-08-31 15:41:22 (星期三) 收件人: xthua/bacant ***@***.***> 抄送: Subscribed ***@***.***> 主题: [xthua/bacant] Number appended after sequence name in annotation.tsv file (Issue #3) 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! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> Xiaoting Hua, PhD, Associate Professor Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Qingchundong 3 RD, Hangzhou 310016, China

[ramadatta]

Hi @xthua

Thank you for reply. Please find the fasta file.

I do not see the version information in the conda installed bacant. I assume it is v3.3.3 installed using this command:

conda install -c bacant -c conda-forge -c bioconda bacant 

Many thanks!

filename.txt

[xthua]

Hi, Prakki: We update BacAnt in Anaconda to 3.3.4. and it support 9999 seqs now, but it is better not to put so much, for Integron_Finder will be very slow. please check it. Best wishes, Xiaoting

…

-----原始邮件----- 发件人:"Prakki Rama" ***@***.***> 发送时间:2022-08-31 17:38:39 (星期三) 收件人: xthua/bacant ***@***.***> 抄送: "Xiaoting Hua" ***@***.***>, Mention ***@***.***> 主题: Re: [xthua/bacant] Number appended after sequence name in annotation.tsv file (Issue #3) Hi @xthua Thank you for reply. Please find the fasta file. I do not see the version information in the conda installed bacant. I assume it is v3.3.3 installed using this command: conda install -c bacant -c conda-forge -c bioconda bacant Many thanks! filename.txt — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***> Xiaoting Hua, PhD, Associate Professor Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Qingchundong 3 RD, Hangzhou 310016, China

[ramadatta]

Hi @xthua ,

Thank you so much! The issue is resolved after bacant update using conda.

I used the following command to update

conda install -c bacant -c conda-forge -c bioconda bacant=3.3.4