[med-svn] [seqsero] 01/03: Add script to anable batch processing easily

[Andreas Tille]

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tille pushed a commit to branch master
in repository seqsero.

commit 29a8a61bde4e29f2d148dd2b0aece632f72cd9ce
Author: Andreas Tille <tille at debian.org>
Date:   Tue Apr 4 09:20:06 2017 +0200

    Add script to anable batch processing easily
---
 debian/bin/seqsero_batch | 41 +++++++++++++++++++++++++++++++++++++++++
 debian/install           |  1 +
 2 files changed, 42 insertions(+)

diff --git a/debian/bin/seqsero_batch b/debian/bin/seqsero_batch
new file mode 100755
index 0000000..eb82828
--- /dev/null
+++ b/debian/bin/seqsero_batch
@@ -0,0 +1,41 @@
+#!/bin/sh
+
+if [ $# != 1 ] ; then
+    echo "Usage: `basename $0` <dir_with_sequence_pairs>"
+    exit
+fi
+
+if [ ! -d $1 ] ; then
+    echo "$1 needs to be a directory"
+    exit
+fi
+
+numR1=`ls $1/*_R1_001.fastq.gz 2>/dev/null | wc -l`
+if [ $numR1 -eq 0 ] ; then
+    echo "No sequences found in directory $1"
+    exit
+fi
+
+numR2=`ls $1/*_R2_001.fastq.gz | wc -l`
+if [ $numR1 -ne $numR2 ] ; then
+    cat <<EOT
+Warning: suspicious number of sequences R1=$numR1 and R2=$numR2
+Both values should be equal.  Please check that are data are valid.
+Continuing processing anyway trying to find matching pairs.
+EOT
+fi
+
+cd $1
+for seq1 in `ls *_R1_001.fastq.gz` ; do
+   seq2=`echo $seq1 | sed 's/_R1_001\.fastq\.gz$/_R2_001.fastq.gz/'`
+   if [ ! -e "$seq2" ] ; then
+      echo "No matching sequence found for $seq1.  File $seq2 does not exist."
+   else
+      check_old_results=`grep "^Input files:[[:space:]]\+\+$seq1 $seq2$" SeqSero_result*/Seqsero_result.txt`
+      if [ "$check_old_results" != "" ] ; then
+         echo "Calculation for $seq1 was done previously and can be found in `echo $check_old_results | sed 's/:Input files.*//'`"
+      else
+         seqsero -m 2 -i "$seq1" "$seq2"
+      fi
+   fi
+done
diff --git a/debian/install b/debian/install
index 775db38..3569847 100644
--- a/debian/install
+++ b/debian/install
@@ -2,3 +2,4 @@ database	usr/share/seqsero
 libs		usr/share/seqsero
 primers		usr/share/seqsero
 SeqSero.py	usr/share/seqsero
+debian/bin	usr

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