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|
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
#Converts KMC usage into man pages. It's a bigger script than the man pages, but the plan is to have a future script that works for all packages
#The man pages are placed in the man folder in the main directory of the kmc package
createManPages();
sub createManPages {
my $source= 'bin';
my $destination= 'man';
my $app_name = 'KMC';
unless ( -d $destination ) {
system(mkdir $destination);
}
my @files;
push(@files,"$source/kmc");
push(@files,"$source/kmc_dump");
if ( scalar @files > 0 ) {
print "Creating manpages\n";
for my $file ( @files ) {
$file =~ s/\n$//;
my $filename = $file;
$filename =~ s/$source\///;
my $uc_filename = uc($filename);
my $man_file = $filename;
$man_file = $destination . '/' . $man_file . '.1';
my $kmc_short_description = q{count kmers in genomic sequences};
my $kmc_long_description = q{KMC—K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.};
my $kmc_dump_short_description = q{list k-mers from kmc-generated database};
my $kmc_dump_long_description = q{KMC's end product is a database of k-mers stored in compact binary form. The kmc_dump program allows the production of a textual list of k-mers together with their counters for the analysis ran};
my $cmd = "help2man -N -m $filename -n $filename --no-discard-stderr $file | sed 's/usage://gi'";
my @output;
push(@output, `$cmd`);
for my $line (@output) {
$line =~ s/\n$//;
}
my @lines_not_to_print;
my @lines_to_print;
if ($filename eq 'kmc') {
my $ss_param_seen = 0;
my $ss_param_seen2 = 1;
my $ip_tag_seen = 0;
for (my $i = 0; $i < scalar @output; $i++) {
my $output_line = $output[$i];
if ($output_line =~ m/^(\.TH\s)([a-zA-Z0-9-]+)(\s.*)/) {
$output_line = $1 . uc($filename) . $3;
}
$output_line =~ s/^(K\-Mer \\- )(kmc)/$2 - $kmc_short_description/;
if ($output_line =~ m/^K\\-Mer Counter/) {
$output_line = $kmc_long_description;
}
if ($output_line =~ m/^\.SS \"Parameters\:\"/ && ! $ss_param_seen) {
push(@lines_not_to_print, $i);
push(@lines_not_to_print, $i + 1);
push(@lines_not_to_print, $i + 2);
push(@lines_not_to_print, $i + 3);
$ss_param_seen = 1;
$ss_param_seen2 = 0;
}
elsif ($output_line =~ m/^\.IP/ && ! $ip_tag_seen) {
$output_line = '.SH SYNOPSIS';
if ($output[$i + 2] =~ /^kmc/) {
$output[$i +2] = ".PP\n" . $output[$i + 2];
}
$ip_tag_seen = 1;
}
elsif ($output_line =~ m/^\.SS ""/) {
push(@lines_not_to_print, $i);
push(@lines_not_to_print, $i + 1);
push(@lines_not_to_print, $i + 2);
push(@lines_not_to_print, $i + 3);
}
elsif ($output_line =~ m/^Example:/) {
$output_line = '.SH EXAMPLES';
$output[$i + 2] = ".PP\n" . $output[$i + 2];
}
elsif ($output_line =~ m/^\.SS \"Parameters\:\"/ && $ss_param_seen && ! $ss_param_seen2) {
last;
}
if ( ! grep( /^$i$/, @lines_not_to_print ) ){
#print "$output_line\n";
push(@lines_to_print, $output_line);
}
}
}
elsif ($filename eq 'kmc_dump') {
my $seen_kmc_start = 0;
my $seen_parameters = 0;
my $seen_options = 0;
my $synopsis_seen = 0;
my @parameters_lines;
my @options_lines;
for (my $i = 0; $i < scalar @output; $i++) {
my $output_line = $output[$i];
if($output_line =~ m/^(\.TH\s)([a-zA-Z0-9-]+)(\s.*)/ ) {
$output_line = $1 . uc($filename) . $3;
}
$output_line =~ s/^(KMC \\- )(kmc_dump)/$2 - $kmc_dump_short_description/;
if ($output_line =~ m/^KMC dump ver\./) {
$output_line = $kmc_dump_long_description;
$seen_kmc_start = 1;
}
if ($output_line =~ m/^kmc/ && $seen_kmc_start == 1 && ! $synopsis_seen) {
$output_line = "\.SH SYNOPSIS\n$output_line";
$synopsis_seen = 1;
}
if ($output_line =~ m/^kmc/ && $seen_kmc_start == 1 && $synopsis_seen) {
push(@lines_not_to_print, $i);
push(@lines_not_to_print, $i + 1);
}
if($output_line =~ m/Parameters:/ && ! $seen_parameters) {
push(@parameters_lines, '.PP');
push(@parameters_lines, $output_line);
push(@parameters_lines, '.PP');
push(@parameters_lines, $output[$i + 1]);
push(@lines_not_to_print, $i);
push(@lines_not_to_print, $i + 1);
$seen_parameters = 1;
}
if($output_line =~ m/Parameters:/ && $seen_parameters) {
push(@lines_not_to_print, $i);
push(@lines_not_to_print, $i + 1);
}
if($output_line =~ m/Options:/ && ! $seen_options) {
push(@options_lines, '.SH OPTIONS');
push(@options_lines, $output[$i + 1]);
push(@options_lines, '.PP');
push(@options_lines, $output[$i + 2]);
push(@lines_not_to_print, $i);
push(@lines_not_to_print, $i + 1);
push(@lines_not_to_print, $i + 2);
$seen_options = 1;
}
if($output_line =~ m/Options:/ && $seen_options) {
push(@lines_not_to_print, $i);
push(@lines_not_to_print, $i + 1);
push(@lines_not_to_print, $i + 2);
}
if ( ! grep( /^$i$/, @lines_not_to_print ) ){
push(@lines_to_print, $output_line);
}
}
for my $line(@options_lines) {
push(@lines_to_print, $line);
}
for my $line(@parameters_lines) {
push(@lines_to_print, $line);
}
}
open (my $man_fh, ">", $man_file);
for my $line(@lines_to_print) {
print $man_fh "$line\n";
}
writeAuthorAndCopyright($man_fh,$filename);
close($man_fh);
print "Manpage creation complete\n";
}
}
}
sub writeAuthorAndCopyright {
my ($man_fh,$filename) = @_;
my $author_blurb = <<END_OF_AUTHOR_BLURB;
.SH "AUTHOR"
.sp
$filename was originally written by:
.PP
Sebastian Deorowicz (sebastian.deorowicz\@polsl.pl)
.PP
Marek Kokot
.PP
Szymon Grabowski
.PP
Agnieszka Debudaj-Grabysz
END_OF_AUTHOR_BLURB
print $man_fh "$author_blurb\n";
my $copyright_blurb = <<'END_OF_C_BLURB';
.SH "COPYING"
.sp
KMC is a free software distributed under GNU GPL3 licence for academic, research, and commercial use.
END_OF_C_BLURB
print $man_fh "$copyright_blurb\n";
}
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