endixk/ezaai

Sequence matched CDS

Opened this issue · 2 comments

PenilCelis commented

Hi all,
I was wondering how I could obtain the sequence of the matched CDS between two genomes.
Thank you in advance,
Arancha

endixk commented

Dear Arancha,
The feature you requested is not supported in the current stable version, however I find it useful and implemented it 😄

Please use this binary: EzAAI_v1.2.2.unstable.jar.zip

To obtain the matching pairs, run the calculate module as following:

java -jar EzAAI_v1.2.2.unstable.jar calculate -i <IN_1> -j <IN_2> -o <OUT> -match <MATCH>

Matching FASTA headers and their sequence identities will be written in the file designated to the -match flag.

You can convert the database into FASTA file as following:

java -jar EzAAI_v1.2.2.unstable.jar convertdb -i <DB> -o <FASTA>

This feature will be included in the next stable release.
Please test out and let me know if you encounter any problem.

PenilCelis commented

Thank you very much! I really appreciate it! It works perfectly fine.