xiangyang1984 / gcluster Goto Github PK

Dear Author,

I noticed that gcluster could be applied for CpG island annotation. I wonder could you please provide an example script?

I want to do CpG island annotation for whole genome. To be specific, huge genome like axolotl (32 Gb). Is it feasible?

Thank you very much and looking forward to your reply.

Best regards,

Xinyu Xiang

Hey,
I really like your tool!

Would it be possible to allow the users to choose the source of label shown on the figure, i.e. choose which qualifier to use, e.g. product instead of locus_tag or genename.

I know this could be modified in TFT file manually but the possibility to control that over the -label flag would be very convenient!

Best

Hallo/ I have been trying to install the package with anacond3, there is a bug where solving the environment always fails, and when I downgrade the anaconda version the package is not available. I tried to download from anaconda navigator, I couldn't find the package. please check thank you very much

Dear Sir/Madam,

I am really interested in using this pipeline, however I found an error every time that I try to run the interested_gene_generation.pl command.

It says everytime the following error:
perl: warning: Falling back to the standard locale ("C").
Can't locate Bio/SeqIO.pm in @inc (you may need to install the Bio::SeqIO module) (@inc contains: /path/for/anaconda3/envs/Gcluster/lib/perl5/site_perl/5.22.0 /lustre7/home/luisafmc/.conda/envs/Gcluster/lib/perl5/5.32/site_perl /lustre7/home/luisafmc/.conda/envs/Gcluster/lib/perl5/site_perl /lustre7/home/luisafmc/.conda/envs/Gcluster/lib/perl5/5.32/vendor_perl /lustre7/home/luisafmc/.conda/envs/Gcluster/lib/perl5/vendor_perl /lustre7/home/luisafmc/.conda/envs/Gcluster/lib/perl5/5.32/core_perl /lustre7/home/luisafmc/.conda/envs/Gcluster/lib/perl5/core_perl .) at interested_gene_generation.pl line 6.
BEGIN failed--compilation aborted at interested_gene_generation.pl line 6.

As I understand it is a problem trying to find the Bio::SeqIO library in the @inc, but I am not really sure.

Thank you for developt this very cool program

In case of missing translation qualifier in CDS features, the amino acid sequence is not generated by interested_gene_generation.pl.

Hi, I came across your program and would like to use it to make nice alignments as in your paper. Installation via conda is fine and the test.pl works but when I try with my own data or your test data I get the error below. Can you please give me clue to resolve this problem. Many thanks Manal

(veiwing) [p170122@PC-228 Gcluster-master]$ Gcluster.pl -dir '/home/p170122/mnt/BactiPipes_MA2017/programs/Gcluster/Gcluster-master/test_data/gbk/' -gene '/home/p170122/mnt/BactiPipes_MA2017/programs/Gcluster/Gcluster-master/test_data/interested_gene_name.txt' -o ~/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest

Tue Jul 14 11:22:27 2020: Gcluster.pl start...

GenBank_extraction_percent: 11...22...33...44...55...66...77...88...100...done
Step 1-1: Extract all predicted proteomic sequences of each genebank file in folder, and transformat protein sequence into a ID-sequence hash

Step 1-2: Extract all feature table of each genebank file in folder
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_arsenitoxydans_3As.tbl_2935.part: File exists.
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_delicata_DSM_16361.tbl_1215.part: File exists.
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_intermedia_ATCC_15466.tbl_248.part: File exists.
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_intermedia_K12.tbl_3085.part: File exists.
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._ACO3.tbl_2878.part: File exists.
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._ACO7.tbl_1889.part: File exists.
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._B1.tbl_3573.part: File exists.
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._FB-Cd.tbl_2821.part: File exists.
Can't do inplace edit on /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_sp._X19.tbl_3231.part: File exists.
Can't open /home/p170122/mnt/REHAB_OR1061/Data_analysis/Chr_AMR/Cattle/RHB12-C24/Gcluster/outputtest/Sub_TFT.gbk/Thiomonas_delicata_DSM_16361.tbl_1215.part: Device not a stream.

Step 2: Generate a sub-TFT table file containing the gene information flanking the interested gene
Device not a stream at /home/p170122/anaconda2/envs/veiwing/share/Gcluster/lib/process.pm line 402, line 62704.

Hello Xiangyang,

Thanks for creating and sharing this tool. I have a few questions regarding using Gcluster, first is in terms of using interested_gene_file.pl, are we supposed to create a fasta file by our own containing the LOCUS tag and protein sequence? Do you have an included script in Gcluster for doing that? Secondly, as I'm thinking of comparing biosynthetic gene clusters, some of the gbk files in my database have identical LOCUS tags, would this situation cause any unwanted crashes from Gcluster?

Kindly regards

Gcluster的作者您好，

非常感谢您能够制作并分享Gcluster。关于Gcluster，我有几个问题希望能够请教您：第一是请问运行interested_gene_file.pl所需的fasta文件是需要包含所有想要比对的gbk文件中的LOCUS标签和蛋白质序列吗？您的package中有包含自动生成这一fasta文件的script吗？第二是请问如果我的database当中有几个gbk文件有相同的LOCUS标签会导致程序运行错误吗？谢谢！