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!

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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