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Fixing spaces.

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1 parent 23fea36 commit 62d82f781cc18a73400a60952ce8df19e86bba31 mestato committed Jul 3, 2015
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Showing with 40 additions and 42 deletions.
  1. +40 −42 hwg_gssr_scripts/findSSRs_post_assembly.pl
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82 hwg_gssr_scripts/findSSRs_post_assembly.pl
@@ -19,20 +19,20 @@
#
# Also path to the primer3 executable and primer3 config files must be specified
# in the global variables section of the script.
-#
+#
# Usage:
# -----
# Usage: findSSRs.pl <arguments>
#
# The list of arguments includes:
-#
+#
# -f|--fasta_file <fasta_file>
-# Required. The file of the sequences to be searched.
-#
+# Required. The file of the sequences to be searched.
+#
# -m|--masked_file <masked_fasta_file>
# Required. A soft-masked version of the fasta file (soft masked means low
# complexity sequences are in lower case bases.)
-#
+#
# Output:
# ------
# Eight output files are produced:
@@ -47,7 +47,7 @@
# A text file of statistics about the SSRs discovered.
#
# <input-file-name>.ssr_report.txt
-# A tab-delimited file with each SSR. The columns are sequence name,
+# A tab-delimited file with each SSR. The columns are sequence name,
# motif, number of repeats, start position and end position.
#
# <input-file-name>.ssr_report.xlsx
@@ -68,21 +68,21 @@
# <input-file-name>.tetra_primer_report.txt
# A tab-delimited file with sequences with a 4-bp SSR motif. Columns are
# sequence name, motif, start position, end position, left primer,
-# right primer, left primer Tm, right primer Tm, amplicon size, full
+# right primer, left primer Tm, right primer Tm, amplicon size, full
# sequence, masked sequence
#
#
-# Details:
+# Details:
# -------
# By default the script finds:
-# 2 bp motifs repeated from 8 to 40 times,
-# 3 bp motifs repeated from 7 to 30 times,
-# 4 bp motifs repeated from 6 to 20 times,
-#
-# The script only reports SSRs that are not within 15 bases of either
+# 2 bp motifs repeated from 8 to 40 times,
+# 3 bp motifs repeated from 7 to 30 times,
+# 4 bp motifs repeated from 6 to 20 times,
+#
+# The script only reports SSRs that are not within 15 bases of either
# end of the sequence, in order to allow for primer design.
#
-# These parameters may be changed in the "GLOBAL PARAMETERS" part of
+# These parameters may be changed in the "GLOBAL PARAMETERS" part of
# the script.
#
@@ -103,7 +103,7 @@
#--------------
# REPEAT IDENTIFICATION PARAMETERS
-# Specify Motif Frequency
+# Specify Motif Frequency
# Motifs that occur less frequently than indicated below will be ignored.
# A 0 indicates that this motif length will be ignored.
@@ -133,7 +133,7 @@
my $PRIMER_PRODUCT_SIZE_RANGE = "100-200";
-my $PRIMER_OPT_TM = "60.0";
+my $PRIMER_OPT_TM = "60.0";
my $PRIMER_MIN_TM = "55.0";
my $PRIMER_MAX_TM = "65.0";
@@ -171,18 +171,18 @@
my %MOTIFLEN = ('2' => 0,
'3' => 0,
'4' => 0);
-
+
my %MOTIFLEN_w_PRIMERS = ('2' => 0,
'3' => 0,
'4' => 0);
-
+
# Set up the Motif specifications, based on the chosen motif types:.
my @MOTIF_SPECS;
push(@MOTIF_SPECS,[2, $MIN_REPS_2bp, $MAX_REPS_2bp, 'dinucleotides']);
push(@MOTIF_SPECS,[3, $MIN_REPS_3bp, $MAX_REPS_3bp, 'trinucleotides']);
push(@MOTIF_SPECS,[4, $MIN_REPS_4bp, $MAX_REPS_4bp, 'tetranucleotides']);
-
+
my $SSR_COUNT = 0;
my $SSR_w_PRIMER_COUNT = 0;
@@ -245,7 +245,7 @@ sub main{
$ssr_out = "$fasta_file.ssr_report.txt";
$ssr_xlsx = "$fasta_file.ssr_report.xlsx";
$fasta_out = "$fasta_file.ssr_filtered.fasta";
- $fasta_out_multi = "$fasta_file.ssr_multi_seqs.fasta";
+ $fasta_out_multi = "$fasta_file.ssr_multi_seqs.fasta";
$stats_out = "$fasta_file.ssr_stats.txt";
$di_primer_out = "$fasta_file.di_primer_report.txt";
@@ -281,7 +281,7 @@ sub main{
print "done.\n";
close DI;
close TRI;
- close TETRA;
+ close TETRA;
close FASTAOUT;
close FASTAMULTI;
@@ -293,8 +293,6 @@ sub main{
$workbook->close();
print "done.\n";
-
-
}
###############################################################
@@ -371,7 +369,7 @@ sub process_seq{
my $regex = "(([gatc]{$motifLength})\\2{$min_number_of_repeats,})";
## LOOPC
- # run through the sequence and check for this motif spec
+ # run through the sequence and check for this motif spec
while ($seq =~ /$regex/ig) {
# Get the ssr and motif that were found
my $ssr = $1;
@@ -394,7 +392,7 @@ sub process_seq{
# Only store the information if we have never
# seen this starting position before
# or anohter ssr starts within 2 bases of this one
-
+
if (!exists $seen{$contig_name."_ssr".$ssrStart} &&
!exists $seen{$contig_name."_ssr".($ssrStart-1)} &&
!exists $seen{$contig_name."_ssr".($ssrStart-2)} &&
@@ -410,19 +408,19 @@ sub process_seq{
## FOUND A SSR TO REPORT
my $ssr_id = $contig_name."_ssr".$ssrStart;
$seen{$ssr_id} = 1;
-
+
#print "$contig_name\tSSR $ssr";
#print "\tmotif $motif";
#print "\tnoRepeats $noRepeats";
#print "\tssrStart $ssrStart\n";
-
+
if(exists $CONTIG_SSRS{$contig_name}){
push @{ $CONTIG_SSRS{$contig_name} }, $ssrStart;
}
- else{
+ else{
$CONTIG_SSRS{$contig_name} = [$ssrStart];
}
-
+
$SSR_COUNT++;
#print "$contig_name\t$ssr_id\t$motif\t$noRepeats\t$ssrStart\t$ssrEnd\n";
printf $out_fh ("$contig_name\t$motif\t$noRepeats\t$ssrStart\t$ssrEnd\n");
@@ -438,12 +436,12 @@ sub process_seq{
$SSR_STATS{$ssr_id}{NO_REPEATS} = $noRepeats;
$SSR_STATS{$ssr_id}{SEQ} = $seq;
$SSR_STATS{$ssr_id}{SEQM} = $seq_masked;
-
+
my $motiflen = length $motif;
my $tmp = $MOTIFLEN{$motiflen};
$tmp++;
$MOTIFLEN{$motiflen} = $tmp;
-
+
# Increment motif count
foreach my $group (keys %MOTIFS) {
my $motifUC = uc($motif);
@@ -467,7 +465,7 @@ sub process_seq{
} # end while (sequence =~ /$regex/ig);
## LOOPB
- } # end for $index (0 .. (scalar @{$MOTIF_SPECS} - 1))
+ } # end for $index (0 .. (scalar @{$MOTIF_SPECS} - 1))
}
@@ -773,7 +771,7 @@ sub printStats{
foreach my $contig_name (keys %CONTIG_SSRS){
my $starts = scalar @{ $CONTIG_SSRS{$contig_name} };
- if($starts == 1){
+ if($starts == 1){
$SINGLE_SSR_COUNT++;
my @starts = @{ $CONTIG_SSRS{$contig_name} };
my $start = $starts[0];
@@ -787,15 +785,15 @@ sub printStats{
my $SSR_COUNT_w_primers = 0;
foreach my $ssr_id (keys %SSR_STATS){
- if($SSR_STATS{$ssr_id}{FORWARD} =~ /\S/){
+ if($SSR_STATS{$ssr_id}{FORWARD} =~ /\S/){
$SSR_COUNT_w_primers++;
}
}
##--------------------------------------------------------------------
## print text file
open (OUTS, ">".$stats_out) || die "ERROR cannot open $stats_out\n";
-
+
print OUTS 'SSR Summary Report\n';
print OUTS "Analsis of $SEQ_COUNT sequences\n";
print OUTS "$time\n";
@@ -824,7 +822,7 @@ sub printStats{
foreach $group (sort keys %MOTIFLEN){
print OUTS "$group\t$MOTIFLEN{$group}\n";
}
-
+
print OUTS "SSRS with PRIMERS\n";
print OUTS "Number of SSRs identified with successful primer design: $SSR_COUNT_w_primers\n";
print OUTS "Number of sequences with 1 SSR and successful primer design: $SINGLE_SSR_COUNT_w_primers\n";
@@ -844,7 +842,7 @@ sub printStats{
$worksheet->set_column('A:A', 75, $formats->{text});
$worksheet->set_column('B:B', 30, $formats->{text});
-
+
$worksheet->write('A1',"SSR Summary Report for $project", $formats->{header});
$worksheet->write('A2',"Analsis of $SEQ_COUNT sequences", $formats->{text});
$worksheet->write('A3',"$time", $formats->{text});
@@ -890,7 +888,7 @@ sub printStats{
$worksheet->write("A$i", "$group bp", $formats->{text});
$worksheet->write("B$i", $MOTIFLEN{$group}, $formats->{text});
}
-
+
$i++;
$i++;
$worksheet->write("A$i",'SSRs with Primers', $formats->{header});
@@ -921,15 +919,15 @@ sub printStats{
sub createExcelWorkbook{
my $ssr_xlsx = $_[0];
-
+
my $workbook; # the excel workbook
my %formats;
my %header;
my %text;
my %bigheader;
my %highlight;
-
-
+
+
# Create an excel workbook
$workbook = Excel::Writer::XLSX->new("$ssr_xlsx");
@@ -940,7 +938,7 @@ sub createExcelWorkbook{
color => 'black',
align => 'left',
text_wrap => 1);
-
+
%text = (font => 'Calibri',
size => 12,
color => 'black',

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