makefiles/getmakef.pl

   1 #!/bin/env perl
   2 use strict;
   3 #use warnings;
   4 use IO::Unread qw(unread);
   5 use Data::Dump qw(ddx);
   6
   7 die "Usage: $0 <fq.gz path> <out path>\n" if @ARGV < 2;
   8 my ($inp,$outp)=@ARGV;
   9
  10 my $Ref = 'Dasnov3';
  11 my $BwaSai = "bwa aln -l 17 -q 10 $Ref";
  12 my $BwaSam = "bwa sampe -a 800 $Ref";
  13 my $BwaSort = 'perl pickU_sort.pl';
  14 my $BwaRmDup = 'samtools rmdup';
  15 my $readsCounter = '/share/users/huxs/git/toGit/c_cpp/faststater/readsCounter';
  16
  17 opendir my($dh), $inp or die "Couldn't open dir '$inp': $!";
  18 my @files = readdir $dh;
  19 closedir $dh;
  20 # http://perlmeme.org/faqs/file_io/directory_listing.html
  21
  22 @files = grep(/\.f(ast|)q\b/i, @files);
  23
  24 #ddx \@files;
  25
  26 my (%Pairs,@AllTargets);
  27 for ( @files ) {
  28         m~^([^/]+?)([\W_]*?)([12])?(\.f(ast|)q(\.gz)?)$~i or die $_;
  29         my ($m,$rp,$r,$ext) = ($1,$2,$3,$4);
  30         $m =~ s/\W//g and die $m;
  31         print "$1, $2, $3, $4, $5, $6, $7\t$m,$rp,$r,$ext, $_\n";
  32 die unless ($r == 1) or ($r==2);        # no SE now
  33         push @{$Pairs{$m}},[$_,$r];
  34 }
  35 @AllTargets = sort keys %Pairs;
  36
  37 ddx \%Pairs;
  38 ddx \@AllTargets;
  39
  40 open M,'>','Makefile' or die $!;
  41 print M 'all: ',join(' ',@AllTargets,'_AdditionalTG_'),"\n";
  42 my @AdditionalTG;
  43
  44 mkdir 'sai';
  45 mkdir 'sam';
  46 mkdir 'bam';
  47
  48 for my $Target ( @AllTargets ) {
  49         my @Files = @{$Pairs{$Target}};
  50 die if @Files != 2;     # no SE now
  51         my (@fqFiles,@newFiles);
  52         for (@Files) {
  53                 my ($fqname,$read12) = @$_;
  54                 $newFiles[$read12-1] = "${Target}_$read12";
  55                 $fqFiles[$read12-1] = $fqname;
  56                 print M "
  57 sai/${Target}_$read12.sai: $inp$fqname
  58 \t$BwaSai $inp$fqname >sai/${Target}_$read12.sai 2>sai/${Target}_$read12.logsai
  59 \tdate >> sai/${Target}_$read12.logsai
  60
  61 sai/${Target}_$read12.fqstat: $inp$fqname
  62 \t$readsCounter -o sai/${Target}_$read12.fqstat $inp$fqname
  63 ";
  64                 push @AdditionalTG, "sai/${Target}_$read12.fqstat";
  65         }
  66         print M "
  67 sam/${Target}.sam.gz: ",join(' ',map { "sai/$_.sai" } @newFiles),"
  68 \t$BwaSam ",join(' ',(map { "sai/$_.sai" } @newFiles),(map { "$inp$_" } @fqFiles) )," 2>sam/${Target}.logsam |gzip -9c >sam/${Target}.sam.gz
  69 \tdate >> sam/${Target}.logsam
  70 ";
  71         print M "
  72 sam/${Target}.sort.bam: sam/${Target}.sam.gz
  73 \t$BwaSort sam/${Target}.sam.gz sam/${Target}.sort.bam
  74 ";
  75         print M "
  76 bam/${Target}.rmdup.bam: sam/${Target}.sort.bam
  77 \t$BwaRmDup sam/${Target}.sort.bam bam/${Target}.rmdup.bam
  78 ";
  79         print M "${Target}: bam/${Target}.rmdup.bam\n";
  80 }
  81
  82         print M join(' ','_AdditionalTG_:',@AdditionalTG),"\n";
  83 close M;
  84
  85 __END__
  86 perl getmakefln.pl fq/ .