New upstream version 1.13.3+dfsg

MYMETA.yml

nytprof.out

pm_to_blib

doc/prokka-*

bug/

db/cm/*.i1*

db/kingdom/*/sprot.p*

language: perl

sudo: false

perl:

    - "5.26"

install:

    - "cpanm --quiet --notest Time::Piece XML::Simple Digest::MD5 Bio::Perl"

    - "export PATH=$PWD/bin:$PATH"

script:

    - "prokka --version"

    - "prokka --help"

    - "! prokka --doesnotexist"

    - "prokka --depends"

    - "prokka --setupdb"

    - "prokka --listdb"

    - "prokka --cpus 2 --outdir asm --prefix asm test/plasmid.fna"

    - "grep '>' asm/asm.fna"

    - "prokka --cleandb"

#!/usr/bin/env perl

# IN

#>ncbi~~~A7J11_00131~~~A7J11_00131 bifunctional aminoglycoside N-acetyltransferase AAC(3)-Ib/aminoglycoside N-acetyltransferase AAC(6')-Ib''

#ATGAGCATCATTGCAACCGTCAAGATCGGCCCTGACGAAATTTCAGCCATGAGGGCTGTG

#CTCGATCTCTTCGGCAAAGAGTTTGAGGACATTCCAACCTACTCTGATCGCCAGCCGACC

#AATGAGTATCTTGCCAATCTTCTGCACAGCGAGACGTTCATCGCGCTCGCTGCTTTTGAC

# OUT

#>Q92AT0 2.4.1.333~~~~~~1,2-beta-oligoglucan phosphorylase~~~COG3459

#MTMLKEIKKADLSAAFYPSGELAWLKLKDIMLNQVIQNPLENRLSQIYVRAHVGDKIEIYPLLSRDAEVGFNENGVEYRGVVGPFRYSVQMHFHTRGWFYDVTVDGD

use Bio::SeqIO;

use Data::Dumper;

@ARGV or die "USAGE: $0".

  ' $(dirname $(which abricate))/../db/ncbi/sequences'.

  ' > $(dirname $(which prokka))/../db/kingdom/Bacteria/AMR';

my $in  = Bio::SeqIO->new(-fh=>\*ARGV,   -format=>'fasta');

my $out = Bio::SeqIO->new(-fh=>\*STDOUT, -format=>'fasta');

my %seen;

while (my $seq = $in->next_seq) {

  my(undef,$gene,$locustag) = split m"~~~", $seq->id;

  $gene = '' if $gene eq $locustag;

  my $prot = $seq->translate;

  die Dumper($prot) if $prot->seq =~ m/\*./; # check for stop codon in middle

  die Dumper($prot) if $seen{$prot->seq}++;  # check for dupes

  $prot->id($locustag);

  $prot->desc( join('~~~', '', $gene, $prot->desc, '') );

  $out->write_seq($prot);

}