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chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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score in GTF file, parsing problem #9

Closed WardDeb closed 6 years ago

WardDeb commented 6 years ago

Hi,

I've used prodigal to generate some GTF files that I use in SNPgenie downstream. I've noticed that if the score field has an actual value, SNPgenie fails saying that there are no + strand products in the GTF file (the score values are for example 120.5). If I remove the score values (by '.') this problem seems to be fixed.

Kind regards,

Warddeb

singing-scientist commented 6 years ago

Thanks so much for catching this bug, @WardDeb ! I have updated the SNPGenie code — if you don't mind, please let me know if it now works with your original GTF file(s) (i.e., before replacing scores with '.'). If it is still not fixed, please share a sample GTF file, if you're willing, so that I may troubleshoot.

With gratitude, Chase

WardDeb commented 6 years ago

Hi Chase,

Thanks for the quick fix! Problem seems to be resolved.

Kind regards,

Warddeb