dnasko / biobin Goto Github PK

Hey Dan,

Was using the mga2fasta.pl script and I realized that if the input fasta file has duplicated sequence IDs, the script will fail or give an incorrect answer.

Here is what is going wrong (I think):

This line is taking just the ID part of the header

so the $FASTA hash table is keyed on just that part.

So if you have multiple sequences with the same ID, only one of them will be in the hash table.

Then, you'll either get an error in the get_nt_orf function because the length of the sequence is not matching up with the mga output files and so the substr function fails here

Then that function will return an empty $orf, which will then cause the gc function to get a divide by zero error here:

That was kind of a confusing example, but hopefully you get what I'm saying.

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:

• alignment/para_rpsblast.pl
• alignment/para_tblastn.pl
• alignment/para_tblastx.pl

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)

Try running:

./biobin/pcr_products/adapter_searching/demultiplex.pl \
-fasta 0-inputs/2nd_batch_anotop_rtpr_fullpasses_3_accuracy_98_length_250_5000.txt \
-adapter 0-inputs/forward_primers.txt \
-window 40 \
-identity 0.85 \
-outdir 1-demultiplex/ \
--trim

And you'll find:

substr outside of string at ./biobin/pcr_products/adapter_searching/demultiplex.pl line 529.
Use of uninitialized value in subroutine entry at /home/wommacklab/library/lib64/perl5/String/Approx.pm line 254.
Use of uninitialized value in subroutine entry at /home/wommacklab/library/lib64/perl5/String/Approx.pm line 254.
Use of uninitialized value $sequence in substr at ./biobin/pcr_products/adapter_searching/demultiplex.pl line 529.
substr outside of string at ./biobin/pcr_products/adapter_searching/demultiplex.pl line 529.
Use of uninitialized value in subroutine entry at /home/wommacklab/library/lib64/perl5/String/Approx.pm line 254.
Use of uninitialized value in subroutine entry at /home/wommacklab/library/lib64/perl5/String/Approx.pm line 254.
 
 Error! Unable to trim this sequence: m181205_052558_42157_c101475712550000001823318702141957_s1_p0/103922/ccs