Merge branch 'master' of https://github.com/Serulab/Py4Bio

code/ch15_1st/15_4.py

@@ -0,0 +1,11 @@
+from Bio import SeqIO
+
+INPUT_FILE = 'fasta22_out.fas'
+OUTPUT_FILE = 'fasta33.fas'
+
+with open(INPUT_FILE) as in_fh:
+    with open(OUTPUT_FILE, 'w') as out_fh:
+        for record in SeqIO.parse(in_fh,'fasta'):
+            # Modify description
+            record.description += '[Rattus norvegicus]'
+            SeqIO.write([record], out_fh, 'fasta')

code/ch15_1st/15_5.py

@@ -0,0 +1,9 @@
+INPUT_FILE = 'fasta22_out.fas'
+OUTPUT_FILE = 'fasta33.fas'
+
+with open(INPUT_FILE) as in_fh:
+    with open(OUTPUT_FILE, 'w') as out_fh:
+        for line in in_fh:
+            if line.startswith('>'):
+                line = line.replace('\n', '[Rattus norvegicus]\n')
+            out_fh.write(line)

code/ch15_1st/fasta33.fas

@@ -0,0 +1,9 @@
+>SSR86 [ssr] : Tomato-EXPEN 2000 map, chr 3[Rattus norvegicus]
+AGGCCAGCCCCCTTTTCCCTTAAGAACTCTTTGTGAGCTTCCCGCGGTGGCGGCCGCTCT
+AG
+>SSR252 [ssr][Rattus norvegicus]
+TGGGCAGAGGAGCTCGTANGCATACCGCGAATTGGGTACACTTACCTGGTACCCCACCCG
+GGTGGAAAATCGATGGGCCCGCGGCCGCTCTAGAAGTACTCTCTCTCT
+>SSR257 [ssr][Rattus norvegicus]
+TGAGAATGAGCACATCGATACGGCAATTGGTACACTTACCTGCGACCCCACCCGGGTGGA
+AAATCGATGGGCCCGCGGCC