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mbshah / ncim-bioinfo

CSIR_NCL_NCIM repo
GNU General Public License v3.0
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Confirm that use of BLAST's `-max_target_seqs` is intentional #1

Open armish opened 5 years ago

armish commented 5 years ago

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you! -- Arman (armish/blast-patrol)

mbshah commented 4 years ago

Hi Amish, Sorry for the late reply, I just saw this. I would like to point out that the virCodes/virfindercommands.txt is not a script, it was just a text file i kept to define basic steps in the script I wrote, and that option has not been included in the final script. Additionally thank you for noticing and informing coders of such errors, it is a great service to the bioinformatic community.