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 ef217c559298293d0fdec522e77b9d46c1af535e..e09efde94bda61796dd7bf44fd63c2622312e612 100755 (executable)
--- 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 33f0a426341b85f04bcbd54f29299491c5aa335d..99f89e8290a247c779d71469b7c2fcb9f7ec66d2 100755 (executable)
--- 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 64c9182cde053a7af648eca3ac2f306d41440d39..0e86c2e431fa4b218899e7739845330d8b2fceea 100644 (file)
--- 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 ]
     }