regex underscore bug in script which produces FASTA_GeckoV2_all.fasta

[stachyra]

Hello,

I think that the downloadable file FASTA_GeckoV2_all.fasta contains a regex-related error, repeated 12 times.

In the original .csv files containing the GeCKOv2 sequences (downloadable from www.addgene.org), there are two gene identifiers which contain an underscore in the gene identifier code itself: "CD99_X" and "CD99_Y". Whatever conversion script you are using to transform from these .csv source files to .fasta format probably contains a regex which is not handling these underscores correctly, because the resulting lines in the fasta file look like this:

CD99_XATACTCACCAGGAAGGGCAT
xatactcaccaggaagggcat
CD99_XGATTTATCCGATGCCCTTCC
xgatttatccgatgcccttcc
CD99_XCTCACCAGCACTGGGTTTCT
xctcaccagcactgggtttct
CD99_YATACTCACCAGGAAGGGCAT
yatactcaccaggaagggcat
CD99_YGATTTATCCGATGCCCTTCC
ygatttatccgatgcccttcc
CD99_YCTCACCAGCACTGGGTTTCT
yctcaccagcactgggtttct
CD99_XATCCCCAAGAAACCCAGTGC
xatccccaagaaacccagtgc
CD99_XAGACTCTTACCGGAGGAACT
xagactcttaccggaggaact
CD99_XTTAGGGGATGACTTTGACTT
xttaggggatgactttgactt
CD99_YATCCCCAAGAAACCCAGTGC
yatccccaagaaacccagtgc
CD99_YAGACTCTTACCGGAGGAACT
yagactcttaccggaggaact
CD99_YTTAGGGGATGACTTTGACTT
yttaggggatgactttgactt

I.e., the label line fails to include an a second underscore between the gene id (CD99_X / CD99_Y) and the 20 bp gRNA sequence, and furthermore the sequence line itself contains an additional prepended "x" or "y".

Best regards,
Andrew L. Stachyra