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hyattpd / Prodigal

Prodigal Gene Prediction Software
GNU General Public License v3.0
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fasta files - empty lines handling #83

Open GaioTransposon opened 3 years ago

GaioTransposon commented 3 years ago

Hi there,

Thank you lots for making this tool! I have maybe an idea for an enhancement.

For some reason I ended up with some empty fasta records. The fasta looks like this (the second record missing):

>T11600_k141_1 flag=1 multi=2.0000 len=446
AAAAGATCAGGTCACTATAT......
>T11600_k141_2 flag=1 multi=16.0000 len=483
--
>T11600_k141_3 flag=1 multi=2.0000 len=476
ATATTATGCAGAACCGGTG......

Prodigal doesn't like it and it just terminates translating when it gets to the "--" point, without any warning.

I can go around it by editing the files so that they would not contain these empty lines, but what also could be possibly an improvement to prodigal could be if it would just skip those lines (and possibly just produce a warning message).

Anyway, thank you!