This is an automated email from the git hooks/post-receive script. jssoares-guest pushed a commit to branch master in repository kmc.
commit 75b0f47d8a6641841e8b3e4ef3bc026cb7ce1df7 Author: Jorge Soares <[email protected]> Date: Tue Nov 18 15:17:06 2014 +0000 Cleanup of dumper statements from usage_to_man script --- debian/usage_to_man | 183 ++++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 134 insertions(+), 49 deletions(-) diff --git a/debian/usage_to_man b/debian/usage_to_man index e69a4bb..33017ab 100755 --- a/debian/usage_to_man +++ b/debian/usage_to_man @@ -3,15 +3,15 @@ use strict; use warnings; use Data::Dumper; -#Converts Fastaq python scripts usage into man pages. -#The man pages are placed in the man folder of the main Fastaq directory +#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= '.'; + my $destination= 'man'; my $app_name = 'KMC'; @@ -37,8 +37,11 @@ sub createManPages { $man_file = $destination . '/' . $man_file . '.1'; - my $kmc_short_description = 'Count kmers in genomic sequences'; - my $kmc_long_description = '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_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'"; @@ -49,68 +52,142 @@ sub createManPages { $line =~ s/\n$//; } - my $ss_param_seen = 0; - my $ss_param_seen2 = 1; - my $ip_tag_seen = 0; + my @lines_not_to_print; my @lines_to_print; + if ($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++) { + for (my $i = 0; $i < scalar @output; $i++) { - my $output_line = $output[$i]; + my $output_line = $output[$i]; - $output_line =~ s/^(\.TH\s)([a-zA-Z0-9-]+)(\s.*)/$1 $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, $i + 3); + if ($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; + $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/^\.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 && ! $ss_param_seen2) { - last; + } + elsif ($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, $output_line); + } - } - if ( ! grep( /^$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); + } + } - print Dumper(\@lines_not_to_print); 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"; } @@ -124,7 +201,15 @@ sub writeAuthorAndCopyright { my $author_blurb = <<END_OF_AUTHOR_BLURB; .SH "AUTHOR" .sp -$filename was originally written by Martin Hunt (mh12\@sanger.ac.uk) +$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"; @@ -132,7 +217,7 @@ END_OF_AUTHOR_BLURB my $copyright_blurb = <<'END_OF_C_BLURB'; .SH "COPYING" .sp -Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&. +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"; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/kmc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
