How to extract the CDS sequences of all LTRs? about tesorter HOT 7 CLOSED

@wensulin93 this seems to be a generic task, you may try agat: https://www.biostars.org/p/9465973/

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You may just use the concatenated domain CDS sequences for each LTR, or the region start at the first domain and end at the last domain (CM030788.1 10392696 - 10396473 ), or the entire LTR (CM030788.1:10391873..10397114) sequence.

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Excellent advice, lucky you can see this post! @oushujun

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@wensulin93 this seems to be a generic task, you may try agat: https://www.biostars.org/p/9465973/

Hello, I thought about this question carefully yesterday. It might help you optimize your software.
Because the genome of the selected species is incomplete (including much information missing from the genomic GFF3 file), it seems that extracting CDS is not an easy task.
I looked at the genetic structure of one LTR. It is found that all the sequences generated by the corresponding.dom. Gff3 file are not complete CDS sequences after splicing together, but they cover most of them. The main parts not covered are the beginning (including ATG) or the end or whatever. However, in the LTR sequence I observed, the EXACT division of CDS sequence was not observed in the GFF3 file of the genome, or even directly skipped that section (not shown in the GFF file). This represents an incomplete GFF file for the genome.
Therefore, if there is no new progress, I will splicing the CDS sequences of all domains together and perform synteny analysis with MCscanX. The ultimate goal is to perform synteny analysis. I think stitching together CDS sequences of all domains will also give me the ideal synteny data. @zhangrengang

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I tried the concatenate_domains.py script, but I got an error message like this:

Traceback (most recent call last):
File "/home/manager/miniconda3/bin/concatenate_domains.py", line 33, in
sys.exit(load_entry_point('TEsorter==1.4.1', 'console_scripts', 'concatenate_domains.py')())
File "/home/manager/miniconda3/bin/concatenate_domains.py", line 25, in importlib_load_entry_point
return next(matches).load()
StopIteration

@zhangrengang

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@wensulin93
Yes, TEsorter do not define the EXACT start, end, or division positions of domains. But these are not neccesary for synteny analyses, so previously I gave you three solutions: the first contains only domains, the second contians almost the full GAG-POL except that the start and end regions may be not incomplete, and the second contains full CDS but also incudes non-coding regions.

Regarding the issue of concatenate_domains.py, how do you use the script? It should be used like:

concatenate_domains.py rice6.9.5.liban.rexdb.cls.pep RH RT INT > rice6.9.5.liban.rexdb.cls.pep_RT_RH_INT.aln

In this example, the RH, RT and INT domains are aligned seperately and then concatennated together. The LTR-RTs that do not contain all the three domains will be excluded.

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@wensulin93 Yes, TEsorter do not define the EXACT start, end, or division positions of domains. But these are not neccesary for synteny analyses, so previously I gave you three solutions: the first contains only domains, the second contians almost the full GAG-POL except that the start and end regions may be not incomplete, and the second contains full CDS but also incudes non-coding regions.

Regarding the issue of concatenate_domains.py, how do you use the script? It should be used like:

concatenate_domains.py rice6.9.5.liban.rexdb.cls.pep RH RT INT > rice6.9.5.liban.rexdb.cls.pep_RT_RH_INT.aln

In this example, the RH, RT and INT domains are aligned seperately and then concatennated together. The LTR-RTs that do not contain all the three domains will be excluded.

Hello，
I think I might solve a problem. Tesorter was previously installed with Conda (1.3.0, "Conda Insall Tesorter"). Then I tried to find the "concatenate_domains.py" script. The result is in a "python-scripts" folder in the conda folder. So I typed the command:
~/miniconda3/pkgs/tesorter-1.3.0-py_0/python-scripts/concatenate_domains.py 2_oute.rexdb-plant.cls.pep RT > rt2.aln

Results hint:
"ZSH: / home/manager/miniconda3 / PKGS/tesorter - 1.3.0 - py_0 / python scripts/concatenate_domains.py: bad interpreter: /opt/conda/condabld/tesorter_1604435924377/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold _place: no such file or directory"

And then I realized that the first line seems to be wrong. So I changed it to
"#! /usr/bin/env python"

Then came the reminder:
"Traceback (most recent call last):
File "/home/manager/miniconda3/pkgs/tesorter-1.3.0-py_0/python-scripts/concatenate_domains.py", line 7, in
from .RunCmdsMP import run_cmd
ImportError: attempted relative import with no known parent package"

I didn't find the script ".RunCmdsMP". Finally I found the script in the "modules" folder. I also found that "concatenate_domains.py" in the modules folder only works. Then the instructions were given:
~/miniconda3/pkgs/tesorter-1.3.0-py_0/site-packages/TEsorter/modules/concatenate_domains.py 2_oute.rexdb-plant.cls.pep RT > rt2.aln

The result file was successfully obtained. The conda installation cauesed the problem. Hope it can be reference! Thank you anyway!

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