def buildIdbaStats(infile, outfile):
'''
build idba stats:
N50
Number of scaffolds
Total scaffold length
'''
PipelineMetagenomeAssembly.contig_to_stats(infile, outfile, PARAMS)
def filterContigs(infile, outfile):
'''
filter contigs if specified in .ini file. If not specified
then the pipeline will not remove any but will produce a new
outfile - this is not space efficient and SHOULD BE CHANGED
'''
if not PARAMS["filter"]:
length = 0
else:
length = PARAMS["filter"]
PipelineMetagenomeAssembly.filterContigs(infile, outfile, length)
def runSpades(infile, outfile):
'''
run spades on each track
'''
job_options = " -l mem_free=30G"
statement = PipelineMetagenomeAssembly.Spades().build(infile)
P.run()
def runSoapdenovo(infile, outfile):
'''
run soapdenovo
'''
job_options = "-l mem_free=30G"
statement = PipelineMetagenomeAssembly.SoapDenovo2().build(infile)
P.run()
def runIdba(infile, outfile):
'''
run idba on each track
'''
job_options = " -l mem_free=30G"
statement = PipelineMetagenomeAssembly.Idba().build(infile)
P.run()
def runMetavelvet(infile, outfile):
'''
run meta-velvet on each track
'''
job_options = " -l mem_free=30G"
statement = PipelineMetagenomeAssembly.Metavelvet().build(infile, PARAMS)
P.run()
def poolReadsAcrossConditions(infiles, outfile):
'''
pool reads across conditions
'''
statement = PipelineMetagenomeAssembly.pool_reads(infiles,
outfile)
P.run()
def buildMetaphlanRelativeAbundance(infile, outfile):
'''
metaphlan is a program used in metagenomics. It assigns
reads to clades based on specific genetic markers via
blastn searching
'''
to_cluster = True
# at present the pipeline will take a set of files
# and compute the abundances of different taxonomic groups
# based on ALL reads i.e. paired data are combined into
# a single file for analysis
if PARAMS["metaphlan_executable"] == "bowtie2":
assert os.path.exists(
PARAMS["metaphlan_db"] + ".1.bt2"
), "missing file %s: Are you sure you have the correct database for bowtie2?" % PARAMS[
"metaphlan_db"] + ".1.bt2"
method = "--bowtie2db"
elif PARAMS["metaphlan_executable"] == "blast":
assert os.path.exists(
PARAMS["metaphlan_db"] + "nin"
), "missing file %s: Are you sure you have the correct database for bowtie2?" % PARAMS[
"metaphlan_db"] + "nin"
method = "--blastdb"
statement = PipelineMetagenomeAssembly.Metaphlan().build(infile,
method="rel_ab")
P.run()
def runRay(infile, outfile):
'''
run Ray on each track
'''
job_options = " -l h=!andromeda,h=!cgatgpu1,h=!cgatsmp1,h=!gandalf,h=!saruman \
-pe mpi 10 \
-q all.q "
statement = PipelineMetagenomeAssembly.Ray().build(infile)
P.run()
def pool_out(infiles):
'''
return outfile name dependent on
input pairedness
'''
# AH: patch required when importing pipeline
if len(infiles) == 0:
return ""
out = {"separate": "1",
False: ""}
inf = infiles[0]
paired = PipelineMetagenomeAssembly.PairedData().checkPairs(inf)
if paired:
paired = paired[0]
format = PipelineMetagenomeAssembly.PairedData().getFormat(inf)
outname = "pooled_reads.dir/agg-agg-agg.%s" % format
return outname
def buildContigLengths(infile, outfile):
'''
output lengths for each contig in each of the assemblies
'''
PipelineMetagenomeAssembly.build_scaffold_lengths(infile, outfile, PARAMS)
def buildSoapdenovoConfig(infile, outfile):
'''
run SGA on each track
'''
PipelineMetagenomeAssembly.SoapDenovo2().config(infile, outfile, PARAMS)