def getCommands(self):
AnalysisUtils.checkDiskSpace(self)
if AnalysisUtils.checkInputFiles(self) == False:
raise Exception("Input files [%s] don't exist = can't continue" %
(self.input_files))
command = "java -Xmx1024M -Djava.awt.headless=true -Djava.awt.headlesslib=true -classpath " + self.classpath + " " + " -Dfastqc.output_dir=" + self.working_dir + " uk.ac.babraham.FastQC.FastQCApplication " + self.input_files[
0].input_file
self.commands.append(
AnalysisCommand(command=command,
command_rank=len(self.commands) + 1))
return self.commands
def getCommands(self):
if self.commands and len(self.commands) > 0:
return self.commands
logging.info(" ========> Analysis %20s Getting commands" % (self.name))
self.commands = []
self.expected_output_files = []
self.temp_output_files = []
outdir = self.output_dir
tmpdir = self.working_dir
btbin = self.bowtiebindir + self.bowtiebinname
stbin = self.samtoolsbindir + self.samtoolsbinname
self.calculateSpaceNeeded()
if FileUtils.fileExists(btbin) == False:
raise Exception("Binary file [%s] doesn't exist = can't continue" %
btbin)
if FileUtils.fileExists(stbin) == False:
raise Exception("Binary file [%s] doesn't exist = can't continue" %
stbin)
if AnalysisUtils.checkInputFiles(self) == False:
raise Exception("Input files [%s] don't exist = can't continue" %
(self.input_files))
AnalysisUtils.checkDiskSpace(self)
for fobj in self.input_files:
f = fobj.input_file
try:
if f.endswith(".gz"):
# f = "<( zcat -c " + f + " )"
tmpf = f.replace(".gz", "")
fparts = FileUtils.getFileParts(tmpf)
command = "gunzip -c " + f + " > " + tmpdir + "/" + fparts[
'basename']
self.commands.append(command)
self.temp_output_files.append(tmpf)
f = tmpdir + "/" + fparts['basename']
fparts = FileUtils.getFileParts(f)
fstub = fparts['filestub']
bowtieoutfile = tmpdir + "/" + fstub + ".sam"
samtoolsoutfile = tmpdir + "/" + fstub + ".bam"
if self.param == None:
raise Exception(
"No parameters entered for bowtie = needs -x <genomeindex>"
)
command1 = btbin + " " + self.param + " " + f + " | " + stbin + " view -bS - | " + stbin + " sort - " + tmpdir + "/" + fstub
logging.info(" ========> Analysis %20s command 1 : %s" %
(self.name, command1))
#command2 = stbin + " view -bS " + bowtieoutfile + "| " + stbin + " sort - " + tmpdir + "/" + fstub
# logging.info(" ========> Analysis %20s command 2 : %s" % (self.name,command2))
command2 = stbin + " index " + samtoolsoutfile
logging.info(" ========> Analysis %20s command 3 : %s" %
(self.name, command2))
# self.expected_output_files.append(fstub + ".sam")
self.expected_output_files.append(
AnalysisExpectedOutputFile(expected_output_file=fstub +
".bam"))
self.expected_output_files.append(
AnalysisExpectedOutputFile(expected_output_file=fstub +
".bam.bai"))
self.commands.append(AnalysisCommand(command=command1))
self.commands.append(AnalysisCommand(command=command2))
#self.commands.append(command3)
except Exception as e:
logging.info(
" ========> Analysis %20s Failed building command list [%s]"
% (self.name, e))
raise
return self.commands