Add CLI tutorial stuff.

cli/p3-script-list.txt

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+p3-all-drugs.pl
+p3-all-genomes.pl
+p3-blast.pl
+p3-build-kmer-db.pl
+p3-count.pl
+p3-echo.pl
+p3-extract-gto.pl
+p3-extract.pl
+p3-feature-gap.pl
+p3-feature-upstream.pl
+p3-file-filter.pl
+p3-find-couples.pl
+p3-find-features.pl
+p3-find-in-clusters.pl
+p3-format-results.pl
+p3-function-to-role.pl
+p3-generate-close-roles.pl
+p3-generate-clusters.pl
+p3-genome-fasta.pl
+p3-get-drug-genomes.pl
+p3-get-family-data.pl
+p3-get-family-features.pl
+p3-get-feature-data.pl
+p3-get-feature-group.pl
+p3-get-feature-sequence.pl
+p3-get-features-by-sequence.pl
+p3-get-genome-contigs.pl
+p3-get-genome-data.pl
+p3-get-genome-drugs.pl
+p3-get-genome-features.pl
+p3-get-genome-group.pl
+p3-gto-dna.pl
+p3-gto-fasta.pl
+p3-gto-scan.pl
+p3-gto.pl
+p3-join.pl
+p3-kmer-compare.pl
+p3-list-feature-groups.pl
+p3-list-genome-groups.pl
+p3-login.pl
+p3-match.pl
+p3-merge.pl
+p3-pick.pl
+p3-project-subsystems.pl
+p3-put-feature-group.pl
+p3-put-genome-group.pl
+p3-rast.pl
+p3-related-by-clusters.pl
+p3-rep-prots.pl
+p3-sequence-profile.pl
+p3-set-to-relation.pl
+p3-signature-clusters.pl
+p3-signature-families.pl
+p3-signature-peginfo.pl
+p3-sort.pl
+p3-stats.pl
+p3-tbl-to-fasta.pl

cli/transform-p3-scripts

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+#
+# Read the p3-scripts list; pull the data from github;
+# transform to restructured text and place into the correct location.
+#
+
+use strict;
+use File::Slurp;
+use File::Temp;
+use Data::Dumper;
+use LWP::UserAgent;
+use Pod::POM;
+use Pod::POM::View::Restructured;
+use File::Basename;
+
+my %link_map  = ('P3Utils/ih_options' => ":ref:`cli-input-options`",
+		 'P3Utils::ih_options' => ":ref:`cli-input-options`",
+		 'P3Utils/data_options' => ":ref:`cli-data-options`",
+		 'P3Utils/col_options' => ":ref:`cli-column-options`",
+		 'P3Utils/delim_options' => ":ref:`cli-delimiter-options`",
+		 );
+
+my $ua = LWP::UserAgent->new;
+
+my $url_base = "https://raw.githubusercontent.com/SEEDtk/RASTtk/master/scripts";
+my $out_base = "../docroot/cli_tutorial/command_list";
+
+open(S, "<", "p3-script-list.txt") or die "Cannot open p3-script-list.txt: $!";
+
+my $conv = Pod::POM::View::Restructured->new({namespace => 'cli'});
+
+my %unmapped_links;
+
+while (my $script = <S>)
+{
+    chomp $script;
+    print "$script\n";
+    my $url = "$url_base/$script";
+    my $res = $ua->get($url);
+    if (!$res->is_success)
+    {
+	die "Error " . $res->code . " fetching $url: " . $res->content;
+    }
+
+    my $txt = $res->content;
+    my $tmp = File::Temp->new();
+    print $tmp $txt;
+    close($tmp);
+
+    my $base = basename($script, ".pl");
+    my $out_file = "$out_base/$base.rst";
+
+    $conv->convert_file("$tmp", $base, $out_file, { link => \&handle_link });
+}
+
+if (%unmapped_links)
+{
+    print STDERR "Unmapped links:\n";
+    for my $l (sort keys %unmapped_links)
+    {
+	print STDERR "\t$l\n";
+    }
+}
+
+sub handle_link
+{
+    my($txt) = @_;
+
+    my $link = $link_map{$txt};
+
+    if (defined($link))
+    {
+	return ('', $link);
+    }
+    elsif ($txt =~ /^(p3.*)\.pl$/)
+    {
+	return ('', ":ref:`cli::$1`");
+    }
+    else
+    {
+	$unmapped_links{$txt}++;
+	return $txt;
+    }
+
+}

cli/update-script-list

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+#!/usr/bin/env perl
+
+#
+# Update the script-list file from the list in git that Bruce keeps.
+#
+
+use strict;
+use LWP::UserAgent;
+
+my $url = 'https://raw.githubusercontent.com/SEEDtk/Web/master/Web/Tutorials/p3_script_list.html';
+
+my $ua = LWP::UserAgent->new;
+
+my $res = $ua->get($url);
+
+if (!$res->is_success)
+{
+    die "Error " . $res->code . " fetching $url: " . $res->content;
+}
+
+open(O, ">", "p3-script-list.txt") or die "Cannot write p3-script-list.txt: $!";
+
+my $txt = $res->content;
+while ($txt =~ /module=([^"]+\.pl)/mg)
+{
+    print O "$1\n";
+}
+close(O);