treesak 1.53.3__py3-none-any.whl

TreeSAK/gap_stats.py

@@ -0,0 +1,38 @@
+import argparse
+from Bio import SeqIO
+
+
+gap_stats_usage = '''
+======= gap_stats example commands =======
+
+TreeSAK gap_stats -i msa.fasta
+
+==========================================
+'''
+
+
+def gap_stats(args):
+
+    msa_in_fa = args['i']
+
+    gap_pct_dict = dict()
+    for each_seq in SeqIO.parse(msa_in_fa, 'fasta'):
+        seq_id = each_seq.id
+        seq_str = str(each_seq.seq)
+        gap_pct = seq_str.count('-')*100/len(seq_str)
+        gap_pct = float("{0:.2f}".format(gap_pct))
+        gap_pct_dict[seq_id] = gap_pct
+
+    gap_pct_sorted = sorted(gap_pct_dict.items(), key=lambda x: x[1])
+
+    print('Sequence\tGap')
+    for each_seq in gap_pct_sorted:
+        print('%s\t%s' % (each_seq[0], each_seq[1]))
+
+
+if __name__ == '__main__':
+
+    gap_stats_parser = argparse.ArgumentParser()
+    gap_stats_parser.add_argument('-i', required=True, help='MSA in fasta format')
+    args = vars(gap_stats_parser.parse_args())
+    gap_stats(args)