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URLs for MAXCONTIGIDLEN limit #131

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6 changes: 5 additions & 1 deletion bin/prokka
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Expand Up @@ -51,7 +51,11 @@ my $PROKKA_DOI = '10.1093/bioinformatics/btu153';
my $DBDIR = "$FindBin::RealBin/../db";
my $HYPO = 'hypothetical protein';
my $UNANN = 'unannotated protein';
my $MAXCONTIGIDLEN = 37; # Genbank rule
# http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#LocusB : no explicit limits on SeqID length
# http://www.ncbi.nlm.nih.gov/books/NBK53702/ : recommends to have sequence IDs shorter than 25 characters
# http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html#FASTAFormatforNucleotideSequences : "Please limit the SeqID to 25 characters or less."
# http://www.ncbi.nlm.nih.gov/genomes/static/Annotation_pipeline_README.txt : the entire "gnl|center|<ID1>" string must not be longer than 41 characters
my $MAXCONTIGIDLEN = 37;
my @LOG; # buffer up log lines before we have log file ready

# these should accept .faa on STDIN and write report to STDOUT
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