diff tools/mira4/mira4.py @ 0:32f693f6e741 draft

Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira4/mira4.py	Thu Sep 26 12:23:42 2013 -0400
@@ -0,0 +1,180 @@
+#!/usr/bin/env python
+"""A simple wrapper script to call MIRA and collect its output.
+"""
+import os
+import sys
+import subprocess
+import shutil
+import time
+
+WRAPPER_VER = "0.0.1" #Keep in sync with the XML file
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg+"\n")
+    sys.exit(err)
+
+
+def get_version(mira_binary):
+    """Run MIRA to find its version number"""
+    # At the commend line I would use: mira -v | head -n 1
+    # however there is some pipe error when doing that here.
+    cmd = [mira_binary, "-v"]
+    try:
+        child = subprocess.Popen(cmd,
+                                 stdout=subprocess.PIPE,
+                                 stderr=subprocess.STDOUT)
+    except Exception, err:
+        sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+        sys.exit(1)
+    ver, tmp = child.communicate()
+    del child
+    return ver.split("\n", 1)[0]
+
+
+os.environ["PATH"] = "/mnt/galaxy/downloads/mira_4.0rc2_linux-gnu_x86_64_static/bin/:%s" % os.environ["PATH"]
+mira_binary = "mira"
+mira_ver = get_version(mira_binary)
+if not mira_ver.strip().startswith("4.0"):
+    stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
+if "-v" in sys.argv:
+    print "MIRA wrapper version %s," % WRAPPER_VER
+    print mira_ver
+    sys.exit(0)
+
+
+def log_manifest(manifest):
+    """Write the manifest file to stderr."""
+    sys.stderr.write("\n%s\nManifest file\n%s\n" % ("="*60, "="*60))
+    with open(manifest) as h:
+        for line in h:
+            sys.stderr.write(line)
+    sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("="*60, "="*60))
+
+
+def massage_symlinks(manifest):
+    """Create FASTQ aliases and edit the manifest to use them.
+
+    Short term measure for MIRA 4.0RC2 which depends on data file
+    extensions to decide the file format, and doesn't like *.dat
+    as used in Galaxy.
+    """
+    base = os.path.split(manifest)[0]
+    with open(manifest) as h:
+        lines = h.readlines()
+    f = 0
+    for i, line in enumerate(lines):
+         if not line.startswith("data ="):
+             continue
+         #Assumes no spaces in filename, would they have to be escaped?
+         new_line = "data ="
+         for filename in line[6:].strip().split():
+             if not filename:
+                 continue
+             assert os.path.isfile(filename), filename
+             f += 1
+             alias = os.path.join(base, "input%i.fastq" % f)
+             new_line += " " + alias
+             cmd = "ln -s %s %s" % (filename, alias)
+             if os.system(cmd):
+                 stop_err("Problem creating FASTQ alias:\n%s" % cmd)
+         lines[i] = new_line + "\n"
+    with open(manifest, "w") as h:
+        for line in lines:
+            #sys.stderr.write(line)
+            h.write(line)
+    return True
+
+
+def collect_output(temp, name):
+    n3 = (temp, name, name, name)
+    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
+    if not os.path.isdir(f):
+        log_manifest(manifest)
+        stop_err("Missing output folder")
+    if not os.listdir(f):
+        log_manifest(manifest)
+        stop_err("Empty output folder")
+    missing = []
+    for old, new in [("%s/%s_out.maf" % (f, name), out_maf),
+                     ("%s/%s_out.unpadded.fasta" % (f, name), out_fasta)]:
+        if not os.path.isfile(old):
+            missing.append(os.path.splitext(old)[-1])
+        else:
+            shutil.move(old, new)
+    if missing:
+        log_manifest(manifest)
+        sys.stderr.write("Contents of %r: %r\n" % (f, os.listdir(f)))
+        stop_err("Missing output files: %s" % ", ".join(missing))
+
+def clean_up(temp, name):
+    folder = "%s/%s_assembly" % (temp, name)
+    if os.path.isdir(folder):
+        shutil.rmtree(folder)
+
+#TODO - Run MIRA in /tmp or a configurable directory?
+#Currently Galaxy puts us somewhere safe like:
+#/opt/galaxy-dist/database/job_working_directory/846/
+temp = "."
+#name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
+name = "MIRA"
+manifest, out_maf, out_fasta, out_log = sys.argv[1:5]
+
+#Hack until MIRA v4 lets us specify file format explicitly,
+massage_symlinks(manifest)
+
+start_time = time.time()
+#cmd_list =sys.argv[8:]
+cmd_list = [mira_binary, manifest]
+cmd = " ".join(cmd_list)
+
+assert os.path.isdir(temp)
+d = "%s_assembly" % name
+assert not os.path.isdir(d), "Path %s already exists" % d
+try:
+    #Check path access
+    os.mkdir(d)
+except Exception, err:
+    log_manifest(manifest)
+    sys.stderr.write("Error making directory %s\n%s" % (d, err))
+    sys.exit(1)
+
+#print os.path.abspath(".")
+#print cmd
+
+handle = open(out_log, "w")
+try:
+    #Run MIRA
+    child = subprocess.Popen(cmd_list,
+                             stdout=handle,
+                             stderr=subprocess.STDOUT)
+except Exception, err:
+    log_manifest(manifest)
+    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    #TODO - call clean up?
+    handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    handle.close()
+    sys.exit(1)
+#Use .communicate as can get deadlocks with .wait(),
+stdout, stderr = child.communicate()
+assert not stdout and not stderr #Should be empty as sent to handle
+run_time = time.time() - start_time
+return_code = child.returncode
+handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
+print "MIRA took %0.2f minutes" % (run_time / 60.0)
+if return_code:
+    handle.write("Return error code %i from command:\n" % return_code)
+    handle.write(cmd + "\n")
+    handle.close()
+    clean_up(temp, name)
+    log_manifest(manifest)
+    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
+             return_code)
+handle.close()
+
+#print "Collecting output..."
+collect_output(temp, name)
+
+#print "Cleaning up..."
+clean_up(temp, name)
+
+print "Done"