de878cd5e29e32002ebc64b66d7cf6989091f8ce
angie
  Mon Oct 10 15:46:16 2022 -0700
Another regex tweak for fluff that ends up in GenBank names.  Oh, those crazy [Hh]umans.

diff --git src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
index 91b9a45..1b42933 100755
--- src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
+++ src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
@@ -1,106 +1,106 @@
 #!/usr/bin/env perl
 
 use warnings;
 use strict;
 
 sub usage() {
   print STDERR "usage: $0 ncbi_dataset.plusBioSample.tsv [fasta]\n";
   exit 1;
 }
 
 # Read in metadata for GenBank virus sequences, then stream through fasta; if header already
 # has a well-formed country/isolate/year name after the accession then keep that, otherwise
 # add from metadata.
 
 sub makeName($$$$) {
   my ($host, $country, $isolate, $year) = @_;
   my @components = ();
   if ($host && $isolate !~ m@^$host/@) {
     push @components, $host;
   }
   if ($isolate =~ m@^([A-Za-z ]+/)?[A-Za-z]+/.*/\d+$@) {
     push @components, $isolate;
   } else {
     if ($country) {
       push @components, $country;
     }
     if ($isolate) {
       push @components, $isolate;
     }
     if ($year) {
       push @components, $year;
     }
   }
   return join('/', @components);
 }
 
 # Replace non-human host scientific names with common names
 my %sciToCommon = ( 'Canis lupus familiaris' => 'canine',
                     'Felis catus' => 'cat',
                     'Mustela lutreola' => 'mink', # Netherlands
                     'Neovison vison' => 'mink',   # Denmark
                     'Panthera leo' => 'lion',
                     'Panthera tigris' => 'tiger',
                     'Panthera tigris jacksoni' => 'tiger'
                   );
 
 my $gbMetadataFile = shift @ARGV;
 
 open(my $GBMETA, "<$gbMetadataFile") || die "Can't open $gbMetadataFile: $!\n";
 
 my %accToMeta = ();
 while (<$GBMETA>) {
   my ($acc, undef, $date, $geoLoc, $host, $isoName) = split("\t");
   # Trim to just the country
   $geoLoc =~ s/United Kingdom:(.*)/$1/;
   $geoLoc =~ s/:.*//;
   $geoLoc =~ s/ //g;
   if ($host eq "Homo sapiens") {
     $host = '';
   } elsif (exists $sciToCommon{$host}) {
     $host = $sciToCommon{$host};
   }
   $isoName =~ s@^SARS?[- ]Co[Vv]-?2/@@;
   $isoName =~ s@^hCo[Vv]-19/@@;
   $isoName =~ s@^BetaCoV/@@;
-  $isoName =~ s@^humans?,?/@@;
+  $isoName =~ s@^[Hh]umans?,?/@@;
   $isoName =~ s@/ENV/@/env/@;
   $isoName =~ s@Canis lupus familiaris@canine@;
   $isoName =~ s@Felis catus@cat@;
   $isoName =~ s@Mustela lutreola@mink@;
   $isoName =~ s@Neovison vison@mink@;
   $isoName =~ s@Panthera leo@lion@;
   $isoName =~ s@Panthera tigris@tiger@;
   $isoName =~ s@Panthera tigris jacksoni@tiger@;
   $isoName =~ s@^COG-UK/@@;
   $accToMeta{$acc} = [$date, $geoLoc, $host, $isoName];
 }
 close($GBMETA);
 
 while (<>) {
   if (/^>([A-Z]+\d+\.\d+)\s*(\S+.*)?\s*$/) {
     my ($acc, $fName) = ($1, $2);
     if (exists $accToMeta{$acc}) {
       my ($mDate, $mCountry, $mHost, $mName) = @{$accToMeta{$acc}};
       my $mYear;
       if ($mDate =~ /^(\d\d\d\d)/) {
         $mYear = $1;
       }
       my $name = makeName($mHost, $mCountry, $mName, $mYear);
       print ">$acc |$name\n";
     } else {
       print STDERR "No metadata for $acc\n";
       s/ / \|/;
       print;
     }
   } elsif (/^[A-Z]+$/) {
     print;
   } else {
     if (/^>/) {
       s/ / \|/;
     } else {
       warn "Passing through weird line:\n$_";
     }
     print;
   }
 }