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Multiple EC_number tags for CDSs, lower case initials in /product descriptions for prokka-1.9.1-testing #18

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Multiple EC_number tags for CDSs, lower case initials in /product descriptions for prokka-1.9.1-testing #18

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a134f08
Enable multiple EC_number tags; lower case initials in /product descr…
aleimba May 30, 2014
7a2d819
Update ChangeLog.txt
aleimba May 30, 2014
7bd434e
minor syntax change in regex to lower case initials in /product desc
aleimba Jun 24, 2014
88bd053
bug fix for option '--hypo' in 'prokka-genbank_to_fasta_db'
aleimba Nov 26, 2014
55be7d3
fixed translation in prokka and prokka-genbank_to_fasta_db
aleimba Dec 4, 2014
13a4066
typo in last commit for "prokka-genbank_to_fasta_db"
aleimba Dec 4, 2014
73e2947
fixed some more syntax errors in \'prokka-genbank_to_fasta_db\', jeez
aleimba Dec 4, 2014
9e94787
added '-' in front of translation option 'complete' bug fixes for con…
aleimba Dec 4, 2014
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249 changes: 129 additions & 120 deletions bin/prokka
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11 changes: 8 additions & 3 deletions bin/prokka-biocyc_to_fasta_db
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,12 @@ while (<$ec_fh>) {
my @x = split m/\t/;
next unless exists $seq{ $x[1] };
next unless $x[7] =~ m/^EC:(.*)$/;
$seq{$x[1]}{EC} = $1;
if ($seq{$x[1]}{EC}) { # concatenate EC_numbers via ';' if several present
next if ($seq{$x[1]}{EC} =~ /$1/); # skip EC numbers that are already included
$seq{$x[1]}{EC} .= ";$1";
} else {
$seq{$x[1]}{EC} = $1;
}
}

while (<$gene_fh>) {
Expand All @@ -41,7 +46,7 @@ while (<$gene_fh>) {
# remove HTML markup
$x[3] =~ s/<.*?>//g;
# special case for regular entities
$x[3] =~ s/&(alpha|beta|gamma|delta|epsilon);/$1/g;
$x[3] =~ s/&(alpha|beta|gamma|delta|epsilon);/$1/g;
# http://stackoverflow.com/questions/576095/how-can-i-decode-html-entities
$x[3] = unidecode(decode_entities($x[3]));
$seq{$id}{PRODUCT} = $x[3];
Expand Down Expand Up @@ -112,5 +117,5 @@ sub usage {
}
exit(1);
}

#----------------------------------------------------------------------
33 changes: 16 additions & 17 deletions bin/prokka-genbank_to_fasta_db
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Expand Up @@ -3,8 +3,10 @@ use strict;
use Bio::SeqIO;
use Data::Dumper;

my(@Options, $verbose, $format, $hypo, $idtag, $sep, $blank, $pseudo, $minlen);
my(@Options, $verbose, $format, $gcode, $hypo, $idtag, $sep, $blank, $pseudo, $minlen);
setOptions();
($gcode < 1 or $gcode > 24) and die "Invalid genetic code, must be 1..24\n";
print STDERR "Using genetic code table $gcode.\n";

my $in = Bio::SeqIO->new(-fh=>\*ARGV, -format=>$format);
my $out = Bio::SeqIO->new(-fh=>\*STDOUT, -format=>'Fasta');
Expand All @@ -13,23 +15,23 @@ while (my $seq = $in->next_seq) {
print STDERR "\rParsing: ",$seq->display_id;
my $counter = 0;
for my $f ($seq->get_SeqFeatures) {

next unless $f->primary_tag eq 'CDS';

next unless $f->length >= $minlen;

next if !$pseudo and $f->has_tag('pseudo');

my $prod = TAG($f, 'product') || $blank;

next if $prod eq 'hypothetical protein';
next if !$hypo and $prod eq 'hypothetical protein';

my $cds = $f->spliced_seq; # don't forget eukaryotes!

my $id = TAG($f, $idtag) or die "feature #$counter does not have /$idtag tag!";
$counter++;
print STDERR "Processing: [$counter] ", $seq->display_id, " | $id | $prod\n" if $verbose;

# HANDLE CODON START FOR FUZZY FEATURES!
if ($f->has_tag('codon_start')) {
my($cs) = $f->get_tag_values('codon_start');
Expand All @@ -41,20 +43,15 @@ while (my $seq = $in->next_seq) {
#END


# DNA -> AA
$cds = $cds->translate;

# remove stop codon
my $aa = $cds->seq;
$aa =~ s/\*$//;
$cds->seq($aa);

# DNA -> AA
$cds = $cds->translate(-codontable_id=>$gcode, -complete => 1);

my $ec = TAG($f, 'EC_number') || $blank;
my $gene = TAG($f, 'gene') || $blank;

$cds->desc("$ec$sep$gene$sep$prod");
$cds->display_id($id);

$out->write_seq($cds);
}
print STDERR "\n";
Expand All @@ -69,6 +66,7 @@ sub TAG {
# Seems new submissions have 2 protein IDs - one useful and one annoying!
# /protein_id="REF_PRJNA193299:EFAU085_p1001"
# /protein_id="YP_008390691.1"
return join(';', $f->get_tag_values($tag)) if ($tag eq 'EC_number'); # concatenate EC_numbers via ';' if several present
return ( grep { ! m/PRJNA/ } $f->get_tag_values($tag) ) [0];
}

Expand All @@ -82,6 +80,7 @@ sub setOptions {
{OPT=>"help", VAR=>\&usage, DESC=>"This help"},
{OPT=>"verbose!", VAR=>\$verbose, DEFAULT=>0, DESC=>"Verbose progress"},
{OPT=>"format=s", VAR=>\$format, DEFAULT=>'genbank', DESC=>"Input format"},
{OPT=>"gcode=i", VAR=>\$gcode, DEFAULT=>1, DESC=>"Genetic code / Translation table (1..24)"},
{OPT=>"idtag=s", VAR=>\$idtag, DEFAULT=>'protein_id', DESC=>"What tag to use as Fasta ID"},
{OPT=>"sep=s", VAR=>\$sep, DEFAULT=>'~~~', DESC=>"Separator between EC/gene/product" },
{OPT=>"blank=s", VAR=>\$blank, DEFAULT=>'', DESC=>"Replace empty EC/gene/product with this"},
Expand Down Expand Up @@ -110,5 +109,5 @@ sub usage {
}
exit(1);
}

#----------------------------------------------------------------------
17 changes: 9 additions & 8 deletions bin/prokka-genpept_to_fasta_db
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Expand Up @@ -12,11 +12,11 @@ while (my $seq = $in->next_seq) {
# print STDERR "\rParsing: ",$seq->display_id;
my $counter = 0;
for my $f ($seq->get_SeqFeatures) {

next unless $f->primary_tag eq 'Protein';

next unless $f->length >= $minlen;

next if !$pseudo and $f->has_tag('pseudo');

my $prod = TAG($f, 'product') || $blank;
Expand All @@ -27,16 +27,16 @@ while (my $seq = $in->next_seq) {

# my $id = TAG($f, $idtag) or die "feature #$counter does not have /$idtag tag!";
my $id = $seq->accession;

$counter++;
print STDERR "Processing: ", $seq->display_id, " | $counter | $id | $prod\n" if $verbose;

my $ec = TAG($f, 'EC_number') || $blank;
my $gene = TAG($f, 'gene') || $blank;

$cds->desc("$ec$sep$gene$sep$prod");
$cds->display_id($id);

$out->write_seq($cds);
}
# print STDERR "\n";
Expand All @@ -48,6 +48,7 @@ print STDERR "\nDone\n";
sub TAG {
my($f, $tag) = @_;
return unless $f->has_tag($tag);
return join(';', $f->get_tag_values($tag)) if ($tag eq 'EC_number'); # concatenate EC_numbers via ';' if several present
return ($f->get_tag_values($tag))[0];
}

Expand Down Expand Up @@ -89,5 +90,5 @@ sub usage {
}
exit(1);
}

#----------------------------------------------------------------------
9 changes: 5 additions & 4 deletions bin/prokka-hamap_to_hmm
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Expand Up @@ -32,7 +32,7 @@ while (<$fam_fh>) {
if (m{^//}) {
#print STDERR "AC=$AC EC=$EC Bac=$Bac\n";
if ($AC and $EC and exists $DESC{$AC}) {
$DESC{$AC} = $EC.$DESC{$AC};
$DESC{$AC} = $EC.$DESC{$AC};
}
if ($AC and ! $Bac) {
print STDERR "Removing $AC as non-Bacterial\n";
Expand All @@ -44,7 +44,8 @@ while (<$fam_fh>) {
$AC = $1;
}
elsif (m/EC=([\d.]+);/) {
$EC = $1;
$EC .= ";$1" if ($EC && $EC !~ $1); # include each EC_number only once
$EC = $1 if (!$EC);
}
elsif (m/^ Bacteria/) {
$Bac = 1;
Expand Down Expand Up @@ -131,12 +132,12 @@ sub setOptions {
}

sub usage {
print "Usage: $0 [options] [--datadir hamap_data_subdir] > hamap.hmm\n";
print "Usage: $0 [options] [--datadir hamap_data_subdir]\n";
foreach (@Options) {
printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
}
exit(1);
}

#----------------------------------------------------------------------
46 changes: 22 additions & 24 deletions bin/prokka-uniprot_to_fasta_db
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Expand Up @@ -8,15 +8,15 @@ use Data::Dumper;
my(@Options, $verbose, $frag, $evlev, $minlen, $sep, $blank, $term, $hypo);
setOptions();

my $HYPO = 'hypothetical protein';
my $HYPO = 'hypothetical protein';

# Read an entire record at a time
local $/ = "\n//\n";

my $in=0;
my $out=0;

while (<ARGV>)
while (<ARGV>)
{
# Read the entry
my $entry = SWISS::Entry->fromText($_);
Expand All @@ -28,17 +28,17 @@ while (<ARGV>)

# Too short?
next if $minlen > 0 and length($entry->SQs->seq) < $minlen;

# Reject on evidence level
# grep ^PE uniprot_sprot.dat | sort | uniq -c
# 74284 PE 1: Evidence at protein level;
# 67762 PE 2: Evidence at transcript level;
# 376894 PE 3: Inferred from homology;
# 14424 PE 4: Predicted;
# 1884 PE 5: Uncertain;
if ($evlev < 5) {
if ($evlev < 5) {
$entry->PE->text =~ m/^(\d+)/;
next unless $1 <= $evlev;
next unless $1 <= $evlev;
}

# Only specified organism class
Expand All @@ -47,31 +47,29 @@ while (<ARGV>)
next unless grep { $_ eq $term } @$tax ;
}

# /gene code
# /gene code
my $gene = $entry->GNs->getFirst || '';
$gene = '' if $gene =~ m/\d{2}/ or $gene =~ m/\./;

my $ec = '';
# my $prod = 'hypothetical protein';
my $prod = '';
my $ec = '';
# my $prod = 'hypothetical protein';
my $prod = '';

if (1) {
for my $de ($entry->DEs->elements) {
if ($de->type eq 'EC') {
$ec = $de->text;
$ec =~ s/^\D*//;
# last;
$ec .= $de->text;
# last;
}
elsif ($de->type eq 'Full' and $de->category eq 'RecName') {
$prod = $de->text;
if ($prod =~ m/^UPF\d|^Uncharacterized protein|^ORF|^Protein /) {
$prod = $HYPO;
}
$prod = $de->text;
if ($prod =~ m/^UPF\d|^Uncharacterized protein|^ORF|^Protein /) {
$prod = $HYPO;
}
}
last if $prod and $ec; # we have some data now, exit out
}
}

$ec =~ s/^\D*//;
$ec =~ s/EC /;/g;

$prod ||= $HYPO;

# skip hypthetical proteins, unless user has overridden this with --hypo
Expand All @@ -80,10 +78,10 @@ while (<ARGV>)
$ec ||= $blank;
$gene ||= $blank;
$prod ||= $blank;

print STDERR join("\t", $entry->AC, $ec, $gene, $prod), "\n" if $verbose;
print ">", $entry->AC, " $ec$sep$gene$sep$prod\n", $entry->SQs->seq, "\n";

$out++;

}
Expand Down Expand Up @@ -121,12 +119,12 @@ sub setOptions {
}

sub usage {
print "Usage: $0 [options] <uniprot.dat>\n";
print "Usage: $0 [options] <uniprot.dat> > sprot\n";
foreach (@Options) {
printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
}
exit(1);
}

#----------------------------------------------------------------------
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