Changeset 58 for liacs/dbdm

Timestamp:

Dec 22, 2009, 8:12:09 AM (15 years ago)

Author:

Rick van der Zwet

Message:

Make the output somehow more clear

File:

• liacs/dbdm/dbdm_4/parse-fasta.py (modified) (1 diff)

liacs/dbdm/dbdm_4/parse-fasta.py

@@ -73 +73 @@
     return(-1,'',head + tail)
 
+# File names
+file1 = "data/AE005174v2-1.fas"
+file2 = "data/AE005174v2-2.fas"
 
 # Get data
-file1 = parse_file("data/AE005174v2-1.fas")
-file2 = parse_file("data/AE005174v2-2.fas")
+seq1 = parse_file(file1)
+seq2 = parse_file(file1)
 
-file1 = fasta.replace(file1)
-file2 = fasta.replace(file2)
+seq1 = fasta.replace(seq1)
+seq2 = fasta.replace(seq2)
 
 # Find overlap
-(retval, common, result) = concat(file2,file1)
+(retval, common, result) = concat(seq2,seq1)
 print retval, common
 
-# Strictly speaking there is a gap of about 4 kbs (4000 bs) between file1 and
-# file2, so lets' put that into the the statistics as well. Due to circular
+print file1
+stats(seq1)
+print file1
+stats(seq1)
+
+# Strictly speaking there is a gap of about 4 kbs (4000 bs) between seq1 and
+# seq2, so lets' put that into the the statistics as well. Due to circular
 # nature, does not matter wether we add it in the beginning or in the end
+print "Total (inc 4 kbs gap (n))"
 result = result + "n" * 4000;
 stats(result)