def detectOrfs(infile, outfile):
statementlist = []
#set job memory and threads
job_memory = str(PARAMS["Prodigal_memory"]) + "G"
job_threads = int(PARAMS["Prodigal_threads"])
#command to generate index files
seqdat = PipelineAssembly.SequencingData(infile)
#generate outfile without gz
outfile = outfile.replace(".gz", "")
#ensure input is FASTA
if seqdat.paired == True:
print("Cannot detect ORFs from paired-end reads.")
else:
if seqdat.fileformat == "fastq":
statementlist.append("reformat.sh in={} out={}".format(
infile, "orfs.dir/" + seqdat.cleanname + ".fa"))
infile = "orfs.dir/" + seqdat.cleanname + ".fa"
#generate the call to prodigal
statementlist.append(
PipelineAnnotate.runProdigal(infile, outfile, PARAMS))
#remove the temp FASTA if created
if seqdat.fileformat == "fastq":
statementlist.append("rm {}".format("orfs.dir/" +
seqdat.cleanname + ".fa"))
#compress the outputs
statementlist.append("gzip {}".format(outfile))
statementlist.append("gzip {}".format(
outfile.replace("peptides", "positions")))
statement = " && ".join(statementlist)
P.run(statement)
def detectOrfs(infile, outfile):
statementlist = []
#set job memory and threads
job_memory = str(PARAMS["Prodigal_memory"]) + "G"
job_threads = int(PARAMS["Prodigal_threads"])
#command to generate index files
seqdat = PipelineAssembly.SequencingData(infile)
#ensure input is FASTA
if seqdat.paired == True:
print(
"Prodigal requires single/merged (i.e. not paired-end) reads for ORF detection."
)
else:
if seqdat.fileformat == "fastq":
statementlist.append("reformat.sh in={} out={}".format(
infile, "orfs.dir/" + seqdat.cleanname + ".fa"))
infile = "orfs.dir/" + seqdat.cleanname + ".fa"
#generate the call to prodigal
statementlist.append(
PipelineAnnotate.runProdigal(infile, outfile, PARAMS))
#remove the temp FASTA if created
if seqdat.fileformat == "fastq":
statementlist.append("rm {}".format("orfs.dir/" +
seqdat.cleanname + ".fa"))
statement = " && ".join(statementlist)
P.run(statement)