Hello,
For now I would like to get function from blast program. And now, I already get functions from blast in format XML (-outfmt 5) but It's not work to open with excel. I don't know, how can i convert xml format to tabular format?. Before I can open result in xml format in excel but i think have some problems maybe this result is larger than before result or maybe it have any wrong format in their result because i choose the parameter as -max_target_seqs 1 and then concatenate into a final result.
The command to run blast like this : blastx -query $query -db ${database%.} -max_target_seqs 1 -outfmt 5 >> Result.out5*
I have many queries blast against with many databases that why i use $query and ${database%.*} in above command line.
Thank you very much for helping
Have you tried output format 6?
Blast - Formatting Output
Thank you Radek, I already tried format 6 output. But In result format 6 can not give me in name of function, it's give only ID (like this : KFY72871.1) but I would like to get ID & name of function (like this : KFY72871.1 hypothetical protein V499_07005 [Pseudogymnoascus sp. VKM F-103]). Do you have any suggestion such as adding parameters or another suggestion.
Thank you very much for helping
Sorry I have never done that. But if I had to, I would either do that in two parts (format 6 then add description based on the name using whatever merging function you like) or I would look at the answers from here:
Tools Parsing Ncbi Blast -M 7 Xml Output Format?
The one from Pierre Lindenbaum seems close to what you would like to have.
I hope you will solve your issue.
Thank you a lot for this information. I already open by your link but i cannot understand. Could you explain an overview of method to solve my problem, please? First of all i have to run again in format 6, right? and then.. (i do not know the next step to solve my problem)
If no one else has an efficient solution could you show the first lines of the query/subject fasta files (with the description you want to include in your output?)