def fetch_genome_files(self, params, gbk_dir):
gfu = GenomeFileUtil(self.callback_url)
gbk = gfu.genome_to_genbank({'genome_ref':params['input_file']})
gbk_file = gbk["genbank_file"]["file_path"]
base = ntpath.basename(gbk_file).rsplit(".", 1)[0]
name_gbff = base + ".gbff"
name_gbk = base + ".gbk"
shutil.copy(gbk_file, gbk_dir)
gbff_path = os.path.join(gbk_dir, name_gbff)
gbk_path = os.path.join(gbk_dir, name_gbk)
shutil.move(gbff_path, gbk_path)
return base, gbk_path
def run_CGView(self, ctx, params):
"""
This example function accepts any number of parameters and returns results in a KBaseReport
:param params: instance of mapping from String to unspecified object
:returns: instance of type "ReportResults" -> structure: parameter
"report_name" of String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: output
#BEGIN run_CGView
print('Starting run_kellyhuangCGView function. Params=')
print(params)
# Validating workspace_name and input_file is present
print('Validating parameters.')
if 'workspace_name' not in params:
raise ValueError(
'Parameter workspace_name is not set in input arguments')
workspace_name = params['workspace_name']
if 'input_file' not in params:
raise ValueError(
'Parameter input_file is not set in input arguments')
input_file = params['input_file']
# Set up CCT project_folder
subprocess.call(
"cd /opt/cgview_comparison_tool && ./update_cogs.sh && cgview_comparison_tool.pl -p project",
shell=True)
# Turn genome object to Genbank file
gfu = GenomeFileUtil(self.callback_url)
gbk = gfu.genome_to_genbank({'genome_ref': input_file})
gbk_file = gbk["genbank_file"]["file_path"]
subprocess.call([
"cp", gbk_file,
"/opt/cgview_comparison_tool/project/reference_genome"
])
base = ntpath.basename(gbk_file).rsplit(".", 1)[0]
name_gbff = base + ".gbff"
name_gbk = base + ".gbk"
from_path = "/opt/cgview_comparison_tool/project/reference_genome/" + name_gbff
print("===== from", from_path)
to_path = "/opt/cgview_comparison_tool/project/reference_genome/" + name_gbk
print("===== to", to_path)
subprocess.call(["mv", from_path, to_path])
# Add Genbank file to project_folder/reference_genome
# Generate map from Genbank file
# subprocess.call("cgview_comparison_tool.pl -p project", shell=True)
os.chdir("/opt/cgview_comparison_tool")
proc = subprocess.Popen([
"cgview_comparison_tool.pl", "-p",
"/opt/cgview_comparison_tool/project"
],
stdout=subprocess.PIPE)
# for line in proc.stdout:
# print(line)
proc.wait()
subprocess.call(["cgview_comparison_tool.pl", "-p", " project"],
shell=True)
# Retrieve map PNG from project_folder/maps
subprocess.call([
"cp", "/opt/cgview_comparison_tool/project/maps/medium.png",
self.shared_folder
])
subprocess.call([
"cp", "/opt/cgview_comparison_tool/project/maps/medium.html",
self.shared_folder
])
# Resize image
basewidth = 900
img = Image.open('/opt/cgview_comparison_tool/project/maps/medium.png')
wpercent = (basewidth / float(img.size[0]))
hsize = int((float(img.size[1]) * float(wpercent)))
img = img.resize((basewidth, hsize), Image.ANTIALIAS)
# img = img.resize((600, 600), Image.ANTIALIAS)
img.save('/opt/cgview_comparison_tool/project/maps/medium1.png',
quality=95)
# print("=====", os.listdir("/opt/cgview_comparison_tool/project/maps/"))
subprocess.call([
"cp", "/opt/cgview_comparison_tool/project/maps/medium1.png",
self.shared_folder
])
png_dir = os.path.join(self.shared_folder, 'medium1.png')
png_dir_higher = os.path.join(self.shared_folder, 'medium.png')
html_dir = os.path.join(self.shared_folder, 'medium.html')
png_dict = {'path': png_dir_higher, 'name': 'Circular_Genome_Map_PNG'}
html_dict = {'path': png_dir, 'name': 'Circular Genome Map'}
report_client = KBaseReport(self.callback_url)
report = report_client.create_extended_report({
'direct_html_link_index':
0,
'html_links': [html_dict],
'file_links': [png_dict],
'workspace_name':
params['workspace_name'],
'summary_window_height':
900,
'html_window_height':
900
})
# subprocess.check_output(["cd", "/opt/cgview_comparison_tool"], shell=True)
# proj_output = subprocess.check_output(["pwd"], shell=True)
# print("=====cd /opt/cgview_comparison_tool=====", proj_output)
#
# report = KBaseReport(self.callback_url)
# report_info = report.create({'report': {'objects_created':[],
# 'text_message': params['input_file']},
# 'workspace_name': params['workspace_name']})
output = {
'report_name': report['name'],
'report_ref': report['ref'],
}
#END run_CGView
# At some point might do deeper type checking...
if not isinstance(output, dict):
raise ValueError('Method run_CGView return value ' +
'output is not type dict as required.')
# return the results
return [output]