MLST Legend + ParSNP support

Author: tseemann

bin/nullarbor.pl

@@ -100,6 +100,7 @@
 my $set = Nullarbor::IsolateSet->new();
 $set->load($input);
 msg("Loaded", $set->num, "isolates:", $set->ids);
+$input = File::Spec->rel2abs($input);
 
 if (not $mlst) {
   require_exe( qw'any2fasta.pl bash mash sort head' );
@@ -204,7 +205,7 @@
 };
 
 $make{'report'} = {
-  DEP => 'report/index.html',
+  DEP => [ 'report/index.html' ],
 };
 
 $make{'report/index.html'} = {
@@ -213,7 +214,7 @@
 };
 
 $make{'report/index.md'} = {
-  DEP => [ $REF, qw(yields kraken abricate mlst.tab mlst2.tab denovo.tab core.aln tree.gif distances.tab roary/roary.png) ],
+  DEP => [ $REF, qw(yields kraken abricate mlst.tab mlst2.tab denovo.tab parsnp core.aln tree.gif distances.tab roary) ],
   CMD => "$FindBin::RealBin/nullarbor.pl --name $name --report --indir $outdir --outdir $outdir/report",
 };
 
@@ -361,7 +362,7 @@
 };
 
 $make{"roary"} = { 
-  DEP => "roary/roary.png",
+  DEP => [ "roary/roary.png" ],   
 };
 
 $make{"roary/roary.png"} = { 
@@ -430,17 +431,26 @@
   CMD => "afa-pairwise.pl $make_dep > $make_target",
 };
 
-my $ptree = "parsnp/parsnp.tree";
 $make{"parsnp"} = { 
-  DEP => $ptree,
+  DEP => "parsnp/parsnp.png",
 };
 
-$make{$ptree} = {
+$make{"parsnp/parsnp.png"} = {
+  DEP => "parsnp/parsnp.svg",
+  CMD => "convert $make_dep $make_target"
+};
+
+$make{"parsnp/parsnp.svg"} = {
+  DEP => "parsnp/parsnp.tree",
+  CMD => "nw_display -S -s -w 1024 -l 'font-size:12' -i 'opacity:0' -b 'opacity:0' $make_dep > $make_target",
+};
+
+$make{"parsnp/parsnp.tree"} = {
   DEP => [ $REF, map { "$_/$CTG" } $set->ids ],
   CMD => [ 
     "mkdir -p parsnp/genomes",
     (map { "ln -sf $outdir/$_/contigs.fa $outdir/parsnp/genomes/$_.fa" } $set->ids),
-    "parsnp -p $threads -c -d parsnp/genomes -r $REF -o parsnp",
+    "parsnp -x -p $threads -c -d parsnp/genomes -r $REF -o parsnp",
   ],
 };
 

perl5/Nullarbor/Report.pm

@@ -62,6 +62,15 @@ sub generate {
   #...........................................................................................
   # MLST
 
+  my $mlst_legend = [
+    [ "Legend", "Meaning" ],
+    [ "n", "exact intact allele" ],
+    [ "~n", "novel allele similar to n" ],
+    [ "n?", "partial match to known allele" ],
+    [ "n,m", "multiple alleles" ],
+    [ "-", "allele missing" ],
+  ];
+  
   my $mlst = load_tabular(-file=>"$indir/mlst.tab", -sep=>"\t", -header=>1);
 #  print STDERR Dumper($mlst);
 
@@ -81,6 +90,8 @@ sub generate {
   heading($fh, "MLST");
   save_tabular("$outdir/$name.mlst.csv", $mlst, ",");
   print $fh "Download: [$name.mlst.csv]($name.mlst.csv)\n";
+  print $fh table_to_markdown($mlst_legend, 1);
+  print $fh "<P>\n";
   print $fh table_to_markdown($mlst, 1);
 
   #...........................................................................................
@@ -108,6 +119,8 @@ sub generate {
   unshift @{$mlst2}, [ "Isolate", "Scheme", "Sequence<BR>Type", ("Allele")x($width-3), "Quality" ];
 
   heading($fh, "MLST (new)");
+  print $fh table_to_markdown($mlst_legend, 1);
+  print $fh "<P>\n";
   print $fh table_to_markdown($mlst2, 1);
 
   #...........................................................................................
@@ -380,6 +393,7 @@ sub generate {
   my $snps = load_tabular(-file=>"$indir/distances.tab", -sep=>"\t");
   print $fh table_to_markdown($snps, 1);
 
+
   #...........................................................................................
   # Core SNP density
   my $ref_fai = "$indir/ref.fa.fai";
@@ -408,6 +422,7 @@ sub generate {
     close HIST;
   }
 
+
   #...........................................................................................
   # Pan Genome
   my $roary_ss = "roary/summary_statistics.txt";
@@ -425,13 +440,28 @@ sub generate {
     }
   }
 
+  #...........................................................................................
+  # ParSNP
+  heading($fh, "ParSNP");
+  
+  print $fh "ParSNP aligns assembled contigs and does simplistic recombination filtering\n";
+  print $fh qx(grep 'Total coverage among' $indir/parsnp/parsnpAligner.log);
+  
+  copy("$indir/parsnp/parsnp.tree", "$outdir/$name.parsnp.tree");
+  print $fh "Download: [$name.parsnp.tree]($name.parsnp.tree)\n";
+
+  copy("$indir/parsnp/parsnp.png", "$outdir/$name.parsnp.png");
+  print $fh "![ParSNP tree]($name.parsnp.png)\n";
+
   #...........................................................................................
   # Software
   heading($fh, "Software");
   my @inv = ( [ "Tool", "Version" ] );
-  for my $tool (qw(nullarbor.pl mlst abricate snippy kraken samtools freebayes megahit prokka roary)) {
+  for my $tool (qw(nullarbor.pl mlst abricate snippy kraken samtools freebayes megahit prokka roary parsnp spades.py)) {
     # print $fh "- $tool ```", qx($tool --version 2>&1), "```\n";
     my($ver) = qx($tool --version 2>&1);
+#    ($ver) = qx($tool -V 2>&1) unless $ver =~ m/$tool/i;
+#    ($ver) = qx($tool 2>&1) unless $ver =~ m/$tool/i;
     chomp $ver;
     $ver =~ s/$tool\s*//i;
     $ver =~ s/version\s*//i;