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Recently I've been helping some researchers with their Samsa2 troubles. I've noticed a few students using operands inappropriately leading to some headaches. I know it's hard to account for this stuff but it might be nice to actively help prevent them!
In the file DIAMOND_specific_organism_retriever.py you might consider adding the following check after the -O, sys.argv parsing. I have seen a few students make this mistake.
if target_org_outfile == os.path.basename(__file__): sys.exit("Cannot write to the file we are specifying: target_org_outfile: {}".format(target_org_outfile))
The text was updated successfully, but these errors were encountered:
I will PR the suggestion this weekend if you just want to wait to review the suggestion :)
jfvorwald
changed the title
Bad operand protections
Bad operand protections - DIAMOND_specific_organism_retriever.py can be overwritten when calling it
Mar 6, 2019
Hi Jack,
First, thank you for helping out researchers looking to use this tool! I
do my best to provide support, both here and through the SAMSA Google
group, but I can't get to everyone.
Yes, it would be great if you submit a PR, and I'll take a look and approve
it. Thank you!
Sam
Recently I've been helping some researchers with their Samsa2 troubles. I've noticed a few students using operands inappropriately leading to some headaches. I know it's hard to account for this stuff but it might be nice to actively help prevent them!
In the file
DIAMOND_specific_organism_retriever.py
you might consider adding the following check after the-O
,sys.argv
parsing. I have seen a few students make this mistake.if target_org_outfile == os.path.basename(__file__): sys.exit("Cannot write to the file we are specifying: target_org_outfile: {}".format(target_org_outfile))
The text was updated successfully, but these errors were encountered: