def countOrfs(infile, outfile):
feat = "gene_id"
outfile = outfile.replace(".gz", "")
filename = re.match(
r"(\S+).(fasta$|fasta.gz|fasta.1.gz|fasta.1|fna$|fna.gz|fna.1.gz|fna.1|fa$|fa.gz|fa.1.gz|fa.1|fastq$|fastq.gz|fastq.1.gz|fastq.1)",
infile).group(1)
filemap = PipelineEnumerate.enumerateMapper(filename, PARAMS)
mapping = "sample_mappings.dir/{}/{}.mapped.bam".format(
filemap.samplename, filemap.samplename)
#get pairedness
paired = True
num_paired = subprocess.check_output(
["samtools", "view", "-c", "-f 1",
"{}".format(mapping)]).decode(sys.stdout.encoding)
if int(num_paired.strip("\n")) == 0:
paired = False
#generate counts per orf across all samples
job_threads = int(PARAMS["featureCounts_threads"])
job_memory = str(PARAMS["featureCounts_memory"]) + "G"
scratchgtf = PARAMS["featureCounts_tmp"] + filename + ".gtf"
statementlist = []
statementlist.append("zcat {} > {}".format(filemap.shortgtfpath,
scratchgtf))
statementlist.append(
PipelineEnumerate.countFeatures(feat, scratchgtf, paired, outfile,
mapping, PARAMS))
statementlist.append("gzip {}".format(outfile))
statementlist.append("rm -rf {}".format(scratchgtf))
statement = " && ".join(statementlist)
P.run(statement)
def makeBowtieDbs(infile, outfile):
filename = re.match(
r"(\S+).(fasta$|fasta.gz|fasta.1.gz|fasta.1|fna$|fna.gz|fna.1.gz|fna.1|fa$|fa.gz|fa.1.gz|fa.1|fastq$|fastq.gz|fastq.1.gz|fastq.1)",
infile).group(1)
filemap = PipelineEnumerate.enumerateMapper(filename, PARAMS)
#call to bowtie2-build
job_memory = str(PARAMS["BowtieDB_memory"]) + "G"
job_threads = int(PARAMS["BowtieDB_threads"])
statement = PipelineEnumerate.buildBowtieDB(filemap.contigpath,
outfile.replace(".1.bt2l", ""),
PARAMS)
P.run(statement)
def mapSamples(infile, outfile):
filename = re.match(
r"(\S+).(fasta$|fasta.gz|fasta.1.gz|fasta.1|fna$|fna.gz|fna.1.gz|fna.1|fa$|fa.gz|fa.1.gz|fa.1|fastq$|fastq.gz|fastq.1.gz|fastq.1)",
infile).group(1)
filemap = PipelineEnumerate.enumerateMapper(filename, PARAMS)
#get the mapping DB
bowtiedb = "contig_databases.dir/{}.contigs.bowtie".format(
filemap.samplename)
job_threads = int(PARAMS["Bowtie_threads"])
job_memory = str(PARAMS["Bowtie_memory"]) + "G"
seqdat = PipelineAssembly.SequencingData(infile)
bowtie = PipelineFilter.Bowtie2(seqdat, outfile, PARAMS, bowtiedb)
#need to reset the working directory in the bowtie function as it is running on files in one directory
bowtie.indir = ""
statementlist = []
#remove all comments from read names in files (trimming can add comments making non-matching pairs)
#only skip if there was a failure in a previous run at the bowtie step
if PARAMS["Bowtie_skip_file_prep"] != "true":
statementlist.append(bowtie.cleanNames())
#directory for output
statementlist.append("mkdir -p {}".format(os.path.dirname(outfile)))
#call to bowtie
statementlist.append(bowtie.build())
#convert sam to bam
statementlist.append("samtools view -bS {} > {}".format(
outfile.replace(".bam", ".sam"), outfile))
#remove the sam file
statementlist.append("rm {}".format(outfile.replace(".bam", ".sam")))
statement = " && ".join(statementlist)
P.run(statement)
def countOrfs(infile, outfile):
feat = "gene_id"
filename = re.match(
r"(\S+).(fasta$|fasta.gz|fasta.1.gz|fasta.1|fna$|fna.gz|fna.1.gz|fna.1|fa$|fa.gz|fa.1.gz|fa.1|fastq$|fastq.gz|fastq.1.gz|fastq.1)",
infile).group(1)
filemap = PipelineEnumerate.enumerateMapper(filename, PARAMS)
mapping = "sample_mappings.dir/{}/{}.mapped.bam".format(
filemap.samplename, filemap.samplename)
#get pairedness
paired = True
num_paired = subprocess.check_output(
["samtools", "view", "-c", "-f 1",
"{}".format(mapping)]).decode(sys.stdout.encoding)
if int(num_paired.strip("\n")) == 0:
paired = False
#generate counts per orf across all samples
job_threads = int(PARAMS["featureCounts_threads"])
job_memory = str(PARAMS["featureCounts_memory"]) + "G"
statement = PipelineEnumerate.countFeatures(feat, filemap.shortgtfpath,
paired, outfile, mapping,
PARAMS)
P.run(statement)
def countPairedFeatures(infile, outfile):
filename = re.search("orf_counts.dir/(\S+).tsv", infile).group(1)
filemap = PipelineEnumerate.enumerateMapper(filename, PARAMS)
#generate counts for other features from ORF counts and full GTF
job_threads = int(PARAMS["featureCounts_threads_otherfeats"])
job_memory = str(PARAMS["featureCounts_memory_otherfeats"]) + "G"
statement = "python {}scripts/countFeatPairs.py --orf_counts {} --feature_pairs {} --gtf {} --outdir annotation_counts.dir/ --logfile {}".format(
os.path.dirname(__file__).rstrip("pipelines"), infile,
",".join(FEATUREPAIRS), filemap.gtfpath, outfile)
#count the tpm counts if enabled
if PARAMS["General_tpm"] == "true":
statement += " && python {}scripts/countFeatPairs.py --orf_counts {} --feature_pairs {} --gtf {} --outdir annotation_counts.dir/ --logfile {}".format(
os.path.dirname(__file__).rstrip("pipelines"),
infile.replace(".tsv", ".tpm.tsv"), ",".join(FEATUREPAIRS),
filemap.gtfpath, outfile.replace(".log", ".tpm.log"))
P.run(statement)