# HG changeset patch
# User dave
# Date 1553101721 14400
# Node ID 3e9704b9d49e9dcba46f0b534c6a29db35c0d1e9
# Parent  1b624d47d9358493bd1b775a84a8c1c090f99b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abayesqr commit f009487e8fec49f10396185ffd2fc4fe65bf4f29-dirty

diff -r 1b624d47d935 -r 3e9704b9d49e abayesqr.xml
--- a/abayesqr.xml	Mon Mar 18 16:07:22 2019 -0400
+++ b/abayesqr.xml	Wed Mar 20 13:08:41 2019 -0400
@@ -7,7 +7,8 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$reference' input.fasta &&
         ln -s '$input' input.sam &&
-        aBayesQR $abayes_params
+        aBayesQR $abayes_params &&
+        python $__tool_directory__/parse_output.py
         ]]>
     </command>
     <configfiles>
diff -r 1b624d47d935 -r 3e9704b9d49e parse_output.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parse_output.py	Wed Mar 20 13:08:41 2019 -0400
@@ -0,0 +1,21 @@
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Bio import SeqIO
+
+def parse_abayesqr_output(input_text, output_fasta):
+    with open(input_text) as input_file:
+        lines = input_file.readlines()
+    records = []
+    for i, line in enumerate(lines):
+        if i % 2 == 0:
+            freq = float(line.split()[-1])
+            number = int(i/2)+1
+            header = 'haplotype-%d_freq-%f' % (number, freq)
+        if i % 2 == 1:
+            seq = Seq(line.strip())
+            record = SeqRecord(seq, id=header, description='')
+            records.append(record)
+    SeqIO.write(records, output_fasta, 'fasta')
+
+if __name__ == '__main__':
+    parse_abayesqr_output("test_ViralSeq.txt", "haplotypes.fasta")