ch15 WiP

code/ch15_1st/15_2.py

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+from Bio import SeqIO
+
+INPUT_FILE = '../../samples/fasta22.fas'
+OUTPUT_FILE = 'fasta22_out.fas'
+
+def retseq(seq_fh):
+    """
+    Parse a fasta file and store non empty records
+    into the fullseqs list.
+    :seq_fh: File handle of the input sequence
+    :return: A list with non empty sequences
+    """
+    fullseqs = []
+    for record in SeqIO.parse(seq_fh,'fasta'):
+        if len(record.seq)!=0:
+            fullseqs.append(record)
+    return fullseqs
+
+with open(INPUT_FILE) as in_fh:
+    with open(OUTPUT_FILE, 'w') as out_fh:
+        SeqIO.write(retseq(in_fh), out_fh, 'fasta')

code/ch15_1st/fasta22_out.fas

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+>SSR86 [ssr] : Tomato-EXPEN 2000 map, chr 3
+AGGCCAGCCCCCTTTTCCCTTAAGAACTCTTTGTGAGCTTCCCGCGGTGGCGGCCGCTCT
+AG
+>SSR252 [ssr]
+TGGGCAGAGGAGCTCGTANGCATACCGCGAATTGGGTACACTTACCTGGTACCCCACCCG
+GGTGGAAAATCGATGGGCCCGCGGCCGCTCTAGAAGTACTCTCTCTCT
+>SSR257 [ssr]
+TGAGAATGAGCACATCGATACGGCAATTGGTACACTTACCTGCGACCCCACCCGGGTGGA
+AAATCGATGGGCCCGCGGCC