From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 23 Sep 2011 12:27:59 +0000 (+0000)
Subject: fixed patscan_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=fd83727b416c953a89986b3b63034dbe15945b95;p=biopieces.git

fixed patscan_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1535 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index ef217c5..e09efde 100755
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -180,6 +180,8 @@ Biopieces.open(tmp_file, options[:stream_out]) do |input, output|
 
             output.puts record
           end
+        else
+          output.puts record
         end
       else
         output.puts record
diff --git a/bp_scripts/QA_454_report.sh b/bp_scripts/QA_454_report.sh
index 33f0a42..99f89e8 100755
--- a/bp_scripts/QA_454_report.sh
+++ b/bp_scripts/QA_454_report.sh
@@ -115,12 +115,14 @@ for sff_file in $sff_files; do
     echo "" && echo "Locating and counting MID tags ... "
     read_fastq -i $fq_file |
     progress_meter |
+    clip_seq |
     find_mids |
     write_tab -o $table_mid -c -k MID_NUM,MID_SEQ,MID_COUNT -x
 
     echo "" && echo "Locating and counting MID tags for sequences longer than 250 ... "
     read_fastq -i $fq_file |
     progress_meter |
+    clip_seq |
     grab -e 'SEQ_LEN >= 250' |
     find_mids |
     write_tab -o $table_mid_len -c -k MID_NUM,MID_SEQ,MID_COUNT -x
@@ -128,6 +130,7 @@ for sff_file in $sff_files; do
     echo "" && echo "Locating and counting MID tags for sequences longer than 250 and mean score above 20 ... "
     read_fastq -i $fq_file |
     progress_meter |
+    clip_seq |
     grab -e 'SEQ_LEN >= 250' |
     mean_scores |
     grab -e 'SCORES_MEAN >= 20' |
diff --git a/code_perl/Maasha/Common.pm b/code_perl/Maasha/Common.pm
index 64c9182..0e86c2e 100644
--- a/code_perl/Maasha/Common.pm
+++ b/code_perl/Maasha/Common.pm
@@ -736,7 +736,7 @@ sub str_analyze
 
     @composition = Maasha::Common::str_analyze_C( $str ); 
 
-    for ( $i = 32; $i < 128; $i++ ) {          # Only include printable chars
+    for ( $i = 32; $i <= 126; $i++ ) {          # Only include printable chars
         $hash{ chr $i } = $composition[ $i ]
     }