Manage special characters in the header annotations

[ssnn]

Primer names that contain characters that are used as delimiters to separate annotation blocks, are problematic. They interfere with the current split strategy used to parse annotations in the presto headers. One of our users found this issue when using CollpaseSeq.py with primers with names like >IGVH1|AB . One option to handle this situation, is to modify presto.IO.readPrimerFile to replace special characters (, |, =, etc) when it reads in the file.

[Jason Vander Heiden]

Changed in 402b745. @ssnn could you test, please?

(I can run the container pipeline tests - building it now.)

[ssnn]

I think “|” doesn’t work. I used this test data

‌

@M00001:373:000000000-JFY4P:1:1101:8899:1007|SEQORIENT=RC|VPRIMER=VH3 a-space
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCTGGCCCCAGTGGTCAAAGTATCCATCTGTTGGCGTACCAACCACTACCACTGCAGTATTTTCCGCCATTTTCGCACAGTAATACGTGGCGGTGTCCGAGGCCTTCAGACTGTTCCACTGCAGGTATGCGGTGTTGGTGGACTTGTCGACTG
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGG
@M00002:373:000000000-JFY4P:1:1101:8899:1007|SEQORIENT=RC|VPRIMER=VH3/2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCTGGCCCCAGTGGTCAAAGTATCCATCTGTTGGCGTACCAACCACTACCACTGCAGTATTTTCCGCCATTTTCGCACAGTAATACGTGGCGGTGTCCGAGGCCTTCAGACTGTTCCACTGCAGGTATGCGGTGTTGGTGGACTTGTCGACTG
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGG
@M00003:373:000000000-JFY4P:1:1101:8899:1007|SEQORIENT=RC|VPRIMER=VH3=2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCTGGCCCCAGTGGTCAAAGTATCCATCTGTTGGCGTACCAACCACTACCACTGCAGTATTTTCCGCCATTTTCGCACAGTAATACGTGGCGGTGTCCGAGGCCTTCAGACTGTTCCACTGCAGGTATGCGGTGTTGGTGGACTTGTCGACTG
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGG
@M00004:373:000000000-JFY4P:1:1101:8899:1007|SEQORIENT=RC|VPRIMER=VH3|2
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCTGGCCCCAGTGGTCAAAGTATCCATCTGTTGGCGTACCAACCACTACCACTGCAGTATTTTCCGCCATTTTCGCACAGTAATACGTGGCGGTGTCCGAGGCCTTCAGACTGTTCCACTGCAGGTATGCGGTGTTGGTGGACTTGTCGACTG
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGG

‌

[Jason Vander Heiden]

Is this the CollapseSeq step? I think we need to test at the MaskPrimers step. Once the headers have misplaced pipes in them, then it’s too late.

[ssnn]

Yes, this was with CollapseSeq. I will check MaksPrimers.

[ssnn]

Yes, MaskPrimers works.

[Jason Vander Heiden]

Thanks!