Added gzip and stdout support

scripts/phylogeny/pairwise_distances.py

@@ -2,22 +2,28 @@
 '''
 Calculate pairwise leaf distances from a phylogeny
 '''
+from gzip import open as gopen
 from os.path import isdir, isfile
 from sys import argv
 try:
     from treeswift import read_tree_newick
 except:
     print("Unable to import TreeSwift. Install via: pip install treeswift"); exit(1)
 if len(argv) != 3:
-    print("USAGE: %s <input_phylogeny> <output_tsv>" % argv[0]); exit(1)
+    print("USAGE: %s <input_phylogeny> <output_tsv or - for stdout>" % argv[0]); exit(1)
 if not isfile(argv[1]):
     raise ValueError("Input file not found: %s" % argv[1])
 if isfile(argv[2]) or isdir(argv[2]):
     raise ValueError("Output file exists: %s" % argv[2])
 tree = read_tree_newick(argv[1])
 dists = tree.distance_matrix(leaf_labels=True)
 labels = list(dists.keys())
-out = open(argv[2], 'w'); out.write("ID1\tID2\tDistance\n")
+if argv[2].strip() == '-':
+    from sys import stdout as out
+elif argv[2].lower().endswith('.gz'):
+    out = gopen(argv[2], 'wt')
+else:
+    out = open(argv[2], 'w'); out.write("ID1\tID2\tDistance\n")
 for i in range(len(labels)-1):
     u = labels[i]
     for j in range(i+1, len(labels)):