diff --git a/hwg_gssr_scripts/findSSRs_post_assembly.pl b/hwg_gssr_scripts/findSSRs_post_assembly.pl index f7400c5..27b39cc 100755 --- a/hwg_gssr_scripts/findSSRs_post_assembly.pl +++ b/hwg_gssr_scripts/findSSRs_post_assembly.pl @@ -1,8 +1,6 @@ #!/usr/bin/env perl ################################################################################ # Author: Meg Staton & Stephen Ficklin -# Date: Jan 23rd, 2014 -# Version: 1 # # DESCRIPTION # ----------- @@ -263,16 +261,15 @@ sub main{ print "$PRIMER3 < $p3_input > $p3_output\n"; my $status = system("$PRIMER3 < $p3_input > $p3_output"); - print "creating Excel workbook..."; - my ($workbook,$formats) = createExcelWorkbook($ssr_xlsx); - print "done.\n"; - print "parsing primer3..."; parseP3_output($p3_output); print "done.\n"; ##--------------------------------------------------------------- - ## Producing output - Excel and statistics + ## Producing output - statistics + + ##--------------------------------------------------------------- + ## Producing output - Fasta files and flat files # open filehandles open (DI, ">$di_primer_out"); @@ -285,19 +282,24 @@ sub main{ my $tetra_fh = *TETRA; my $fastaout_fh = *FASTAOUT; my $fastamulti_fh = *FASTAMULTI; - - # generate filehandles - my ($di_worksheet, $tri_worksheet, $tetra_worksheet) = initiate_workbooks($workbook, $formats, $project); - - - - print "done.\n"; close DI; close TRI; close TETRA; close FASTAOUT; close FASTAMULTI; + ##--------------------------------------------------------------- + ## Producing output - Excel + + print "creating Excel workbook..."; + my ($workbook,$formats) = createExcelWorkbook($ssr_xlsx); + print "done.\n"; + + print "generate output..."; + # generate filehandles + my ($di_worksheet, $tri_worksheet, $tetra_worksheet) = initiate_workbooks($workbook, $formats, $project); + print "done.\n"; + #print "stats...\n"; #my $worksheet_stats = printStats($stats_out, $workbook, $formats, $project); # @@ -305,7 +307,6 @@ sub main{ #$worksheet_stats->select(); #$workbook->close(); - print "done.\n"; } ############################################################### @@ -672,7 +673,13 @@ sub _initiate_worksheet{ return $worksheet; } +sub _print_worksheet{ + my $worksheet = $_[0]; + my $formats = $_[1]; + my $name = $_[2]; + +} # my $multi_flag = 0; # ## skip contigs with more than one ssr # if(scalar @{ $CONTIG_SSR_STARTS{$contig}} == 1){