--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NEUMA-1.2.1/auto_NEUMA_SE.pl	Thu Aug 08 00:46:13 2013 -0400
@@ -0,0 +1,176 @@
+#!/usr/bin/perl
+
+if(@ARGV<9) { print "usage: $0 [options] -L=<read_length> -i=<input_file> -U=<EUMA_prefix(fullpath, before .gEUMA or .iEUMA)> --g2m=<gene2NM_file> --g2s=<gene2symbol_file> -b=<bowtie_dir(eg.bin/bowtie-0.12.7)> --bi=<bowtieindex> -o=<outputdir> -s=<sample_name>\n\nOrder of arguments can be interchangeable.\n\n"; exit; }
+
+
+
+## options ##
+($fastoption)= grep /^-f=/, @ARGV;
+if(!defined($fastoption)){$fastoption='q'; }
+else { $fastoption =~s/^-f=//; if($fastoption !~/^[fq]$/) { die "wrong file type (-f).\n"; } }
+
+($coding_option)= grep /^-c=/, @ARGV;
+if(!defined($coding_option)){$coding_option='n'; }
+else { $coding_option =~s/^-c=//; if($coding_option !~/^[nc]$/) { die "wrong coding option (-c).\n"; } }
+
+($datatype)= grep /^-d=/, @ARGV;
+if(!defined($datatype)){$datatype='R'; }
+else { $datatype =~s/^-d=//; if($datatype !~/^[RE]$/) { die "wrong data type (-d).\n"; } }
+
+($parallel)= grep /^-p=/, @ARGV;
+if(!defined($parallel)){$parallel=1; }
+else { $parallel =~s/^-p=//; if($parallel !~/^[\d]+$/) { die "wrong parallel (multi-thread) option (-p).\n"; } }
+
+($EUMAcut)= grep /^-t=/, @ARGV;
+if(!defined($EUMAcut)){$EUMAcut=50; }
+else { $EUMAcut =~s/^-t=//; if($EUMAcut !~/^[\d\.]+$/) { die "wrong EUMAcut (-t).\n"; } }
+
+($StrandSpecificity)= grep /^--str=/, @ARGV;
+if(!defined($StrandSpecificity)){ $StrandSpecificity='N'; }
+else { $StrandSpecificity =~s/^--str=//; if($StrandSpecificity !~/^[SRN]+$/) { die "wrong strand specificity (--str).\n"; } }
+
+($get_gReadcount)= grep /^--gReadcount/, @ARGV;
+if(!defined($get_gReadcount)){ $get_gReadcount=0; }
+else { $get_gReadcount=1; }
+
+($mm)= grep /^--mm=/, @ARGV;
+if(!defined($mm)){ $mm=0; }
+else { $mm =~s/^--mm=//; if($mm !~/^[\d\.]+$/) { die "ERROR: wrong number of mismatches (--mm).\n"; } }
+
+($noNIR)= grep /^--noNIR/, @ARGV;
+if(!defined($noNIR)){ $noNIR=0; }
+else { $noNIR=1; }
+
+($noNEUMA)= grep /^--noNEUMA/, @ARGV;
+if(!defined($noNEUMA)){ $noNEUMA=0; }
+else { $noNEUMA=1; }
+
+if($noNIR==1 && $noNEUMA==0) { die "ERROR: --noNIR must be used together with --noNEUMA.\n"; }
+
+
+
+
+## required arguments ##
+
+($READ_LENGTH)= grep /^-L=/, @ARGV;
+if(!defined($READ_LENGTH)){ die "READ_LENGTH must be specified (-L).\n"; }
+else { $READ_LENGTH =~s/^-L=//; if($READ_LENGTH !~/^[\d]+$/) { die "wrong READ_LENGTH (-L).\n"; } }
+
+($input_fa)= grep /^-i=/, @ARGV;
+if(!defined($input_fa)){ die "input_fa must be specified (-i).\n"; }
+else { $input_fa =~s/^-i=//; if(!-e $input_fa) { die "wrong input_file (-i).\n"; } }
+
+($EUMAprefix)= grep /^-U=/, @ARGV;
+if(!defined($EUMAprefix)){ die "EUMAprefix must be specified (-U).\n"; }
+else { $EUMAprefix =~s/^-U=//; if(!-e $EUMAprefix.".gEUMA" || !-e $EUMAprefix.".iEUMA") { die "wrong EUMAprefix (-U).\n"; } }
+
+($gene2NM_file)= grep /^--g2m=/, @ARGV;
+if(!defined($gene2NM_file)){ die "gene2NM_file must be specified (--g2m).\n"; }
+else { $gene2NM_file =~s/^--g2m=//; if(!-e $gene2NM_file) { die "wrong gene2NM_file (--g2m).\n"; } }
+
+($gene2symbol_file)= grep /^--g2s=/, @ARGV;
+if(!defined($gene2symbol_file)){ die "gene2symbol_file must be specified (--g2s).\n"; }
+else { $gene2symbol_file =~s/^--g2s=//; if(!-e $gene2symbol_file) { die "wrong gene2symbol_file (--g2s).\n"; } }
+
+($bowtie_dir)= grep /^-b=/, @ARGV;
+if(!defined($bowtie_dir)){ die "bowtie_dir must be specified (-b).\n"; }
+else { $bowtie_dir =~s/^-b=//;  if(!-d $bowtie_dir || !-e "$bowtie_dir/bowtie") { die "wrong bowtie_dir(please avoid using '~') (-b).\n"; } }
+
+($bowtieindex)= grep /^--bi=/, @ARGV;
+if(!defined($bowtieindex)){ die "bowtieindex must be specified (--bi).\n"; }
+else { $bowtieindex =~s/^--bi=//; if(!-e "$bowtieindex.1.ebwt") { die "wrong bowtieindex (--bi).\n"; } }
+
+($basedir)= grep /^-o=/, @ARGV;
+if(!defined($basedir)){ die "output dir must be specified (-o).\n"; }
+else { $basedir =~s/^-o=//; if($basedir=~/~/) { die "wrong base_dir(please avoid using '~') (-o).\n"; }  }
+
+($sample)= grep /^-s=/, @ARGV;
+if(!defined($sample)){ die "sample name must be specified (-s).\n"; }
+else { $sample =~s/^-s=//;  }
+
+
+##############
+
+
+my $coding='';
+if($coding_option eq 'n') {$coding='';}
+elsif($coding_option eq 'c') {$coding='-C';}
+else { die "Error: invalid coding option.\n"; }
+
+if($datatype eq 'R') { $mapping_stat_column = 1; }
+elsif($datatype eq 'E') { $mapping_stat_column = 3; }
+else { die "Error: wrong datatype.\n"; }
+
+if($StrandSpecificity eq 'S') { $bowtie_strand_option = "--norc"; }
+elsif($StrandSpecificity eq 'R') { $bowtie_strand_option = "--nofc"; }
+else { $bowtie_strand_option = ""; }
+
+
+($scriptdir) = $0 =~ /(.+)\/[^\/]+$/;
+
+$bowtieout_dir = "$basedir/bowtieout";
+$readcount_dir = "$basedir/readcount";
+$FVKMdir = "$basedir/FVKM";
+$LVKMdir = "$basedir/LVKM";
+
+$bowtieoutfile = "$bowtieout_dir/$sample.single.mm$mm.bowtieout";
+$bestbowtieoutfile = "$bowtieout_dir/$sample.single.mm$mm.best.bowtieout";
+$mapping_stat_file = "$basedir/mapping_stat.$sample.single";
+
+`mkdir -p $bowtieout_dir`;
+`mkdir -p $readcount_dir`;
+`mkdir -p $FVKMdir`;
+`mkdir -p $LVKMdir`;
+
+`dos2unix $gene2NM_file`;
+`dos2unix $gene2symbol_file`;
+
+
+#$perlcommand = "perl -I $scriptdir";
+$perlcommand = "perl";
+$bestbowtieout_script = "$scriptdir/filter.best.from.bowtieout.3.pl";
+$bowtieout2mappingstat_script = "$scriptdir/bowtieout2mappingstat.3.pl";
+$bowtieout2readcount_script = "$scriptdir/bowtie2genecount.11.pl";
+$NIR2LVKM_script = " $scriptdir/NIR2LVKM_SE.pl";
+
+=cut
+print STDERR "Mapping reads using bowtie...\n";
+`$bowtie_dir/bowtie -$fastoption $coding -a -v $mm --suppress 5,6,7 -p $parallel -m 100 $bowtie_strand_option $bowtieindex $input_fa > $bowtieoutfile`; 
+
+
+
+print STDERR "Filtering best-matching alignments...\n";
+if($mm > 0) {
+  system("$perlcommand $bestbowtieout_script -d $datatype --rm $bowtieoutfile 0");
+}
+else {
+  system("mv $bowtieoutfile $bestbowtieoutfile");
+}
+
+print STDERR "Computing the mapping stat...\n";
+system("$perlcommand $bowtieout2mappingstat_script -d $datatype $bestbowtieoutfile $sample 0 > $mapping_stat_file");
+print STDERR "Mapping stat :\n";
+system("cat $mapping_stat_file");
+
+if($noNIR==0){
+  system("$perlcommand $bowtieout2readcount_script -d $datatype --gNIR -f -s $sample -v $gene2NM_file $bestbowtieoutfile 0 > $readcount_dir/$sample.mm$mm.gNIR");
+  system("$perlcommand $bowtieout2readcount_script -d $datatype --iNIR -f -s $sample -v $gene2NM_file $bestbowtieoutfile 0 > $readcount_dir/$sample.mm$mm.iNIR");
+}
+=cut
+#if($get_gReadcount==1) { 
+  system("$perlcommand $bowtieout2readcount_script -d $datatype -f -s $sample -v $gene2NM_file $bestbowtieoutfile 0 > $readcount_dir/$sample.mm$mm.gReadcount");
+#}
+
+
+=cut
+
+if($noNEUMA==0){
+  print STDERR "Computing FVKM and LVKM...\n";
+  `$perlcommand $NIR2LVKM_script $sample $readcount_dir mm$mm $EUMAprefix $FVKMdir $LVKMdir $EUMAcut $mapping_stat_column $mapping_stat_file 0 2 $gene2NM_file $gene2symbol_file $datatype $scriptdir`;
+}
+
+print STDERR "Done.\n";
+
+
+
+