Mercurial > repos > galaxyp > scaffold

comparison scaffold_wrapper.py @ 1:0d0cbb69a03f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author galaxyp
date Fri, 26 Sep 2014 15:10:34 -0400
parents e9981e6af666
children
comparison
equal deleted inserted replaced
0:e9981e6af666 1:0d0cbb69a03f
45 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) 45 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
46 returncode = proc.wait() 46 returncode = proc.wait()
47 if returncode != 0: 47 if returncode != 0:
48 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) 48 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
49 finally: 49 finally:
50 print open(tmp_stderr_name, "r").read(64000) 50 print((open(tmp_stderr_name, "r").read(64000)))
51 print open(tmp_stdout_name, "r").read(64000) 51 print((open(tmp_stdout_name, "r").read(64000)))
52 52
53 53
54 def delete_file(path): 54 def delete_file(path):
55 if os.path.exists(path): 55 if os.path.exists(path):
56 try: 56 try:
150 150
151 151
152 def build_samples(samples_file): 152 def build_samples(samples_file):
153 group_data = parse_groups(samples_file, group_parts=["sample", "mudpit", "category"], input_parts=["name", "path", "ext"]) 153 group_data = parse_groups(samples_file, group_parts=["sample", "mudpit", "category"], input_parts=["name", "path", "ext"])
154 samples_description = "" 154 samples_description = ""
155 for sample_name, sample_data in group_data.iteritems(): 155 for sample_name, sample_data in list(group_data.items()):
156 files = sample_data["inputs"] 156 files = sample_data["inputs"]
157 mudpit = sample_data["group_data"]["mudpit"] 157 mudpit = sample_data["group_data"]["mudpit"]
158 category = sample_data["group_data"]["category"] 158 category = sample_data["group_data"]["category"]
159 samples_description += """<BiologicalSample database="database" name="%s" mudpit="%s" category="%s">\n""" % (sample_name, mudpit, category) 159 samples_description += """<BiologicalSample database="database" name="%s" mudpit="%s" category="%s">\n""" % (sample_name, mudpit, category)
160 for (name, path, ext) in files: 160 for (name, path, ext) in files:
305 output_path = options.output 305 output_path = options.output
306 template_parameters["output_path"] = output_path 306 template_parameters["output_path"] = output_path
307 307
308 # Prepare and create driver file 308 # Prepare and create driver file
309 driver_contents = Template(template).substitute(template_parameters) 309 driver_contents = Template(template).substitute(template_parameters)
310 print driver_contents 310 print(driver_contents)
311 driver_path = os.path.abspath("driver.xml") 311 driver_path = os.path.abspath("driver.xml")
312 open(driver_path, "w").write(driver_contents) 312 open(driver_path, "w").write(driver_contents)
313 313
314 # Run Scaffold 314 # Run Scaffold
315 execute("ScaffoldBatch3 '%s'" % driver_path) 315 execute("ScaffoldBatch3 '%s'" % driver_path)