diff tools/mummer/mummer.py @ 0:b0551f2a5986 draft

Uploaded v0.0.1, essentially a preview (previously only on the TestToolShed). No tests yet, no gnuplot or ps2pdf dependency yet.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mummer/mummer.py	Mon Oct 27 12:56:55 2014 -0400
@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+"""MUMmer wrapper calling nucmer/promer/mummerplot etc,
+
+Takes the following command line options,
+1. FASTA filename of species A
+2. FASTA filename of species B
+3. Algorithm, nucmer or promer
+4. PNG output filename
+5. PDF output filename
+"""
+
+import os
+import sys
+import tempfile
+import shutil
+
+def stop_err( msg ):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(1)
+
+def run(cmd):
+    print(cmd)
+    return_code = os.system(cmd)
+    if return_code:
+        stop_err("Error %i from: %s" % (return_code, cmd))
+
+if "-v" in sys.argv [1:]or "--version" in sys.argv[1:]:
+    print("MUMmer wrapper v0.0.1\n")
+    os.system("nucmer --version")
+    os.system("promer --version")
+    os.system("mummerplot --version")
+    sys.exit(0)
+
+#Parse Command Line
+#TODO - optparse
+try:
+    fasta_a, fasta_b, algorithm, png_out, pdf_out = sys.argv[1:]
+except:
+    stop_err("Expect 5 arguments, got %i" % (len(sys.argv) - 1))
+
+
+valid_algo = ["mummer", "nucmer", "promer"]
+if algorithm not in valid_algo:
+    stop_err("Invalid algorithm argument %r, should be: %s" % (algorithm, ", ".join(valid_algo)))
+
+base_path = tempfile.mkdtemp()
+prefix = os.path.join(base_path, "ref_qry")
+coords = prefix + ".mums"
+#gnuplot = prefix + ".gp"
+ps_image = prefix + ".ps"
+png_image = prefix + ".png"
+
+if algorithm == "mummer":
+    #Add -mum as per example to find maximal unique matches between ref and query.
+    #Add the -b -c options to search both strands and report relative to forward strand
+    #which then matches the default dual-strand approach in nucmer and promer
+    cmd = '%s -mum -b -c "%s" "%s" > %s' % (algorithm, fasta_a, fasta_b, coords)
+else:
+    coords = "out.delta"
+    cmd = '%s "%s" "%s"' % (algorithm, fasta_a, fasta_b)
+run(cmd)
+
+# PNG
+# ===
+cmd = 'mummerplot -R "%s" -Q "%s" --png --large --prefix=%s %s' % (fasta_a, fasta_b, prefix, coords)
+run(cmd)
+shutil.move(png_image, png_out)
+
+# PS --> PDF
+# ==========
+# Using --large, puts "set size 3,3" in the gnuplot - which seems to mess up.
+# Problem here is the default bbox (BoundingBox) in the PS output is letter page size,
+# and even if we override that, at least when view the PS output in Adobe Illustrator
+# things don't seem to be lined up properly :(
+#
+# Using "set size 1,1" works better - which is what --small gives:
+cmd = 'mummerplot -R "%s" -Q "%s" --postscript --small --prefix=%s %s' % (fasta_a, fasta_b, prefix, coords)
+run(cmd)
+cmd = 'ps2pdf -dEPSCrop "%s" "%s"' % (ps_image, pdf_out)
+run(cmd)
+
+#Remove temp files...
+os.remove(coords) # Might not be under the temp directory...
+shutil.rmtree(base_path)