def buildIdbaStats(infile, outfile):
'''
build idba stats:
N50
Number of scaffolds
Total scaffold length
'''
PipelineGenomeAssembly.contig_to_stats(infile, outfile, PARAMS)
def buildMetavelvetStats(infile, outfile):
'''
build metavelvet stats:
N50
Number of scaffolds
Total scaffold length
'''
PipelineGenomeAssembly.contig_to_stats(infile, outfile, PARAMS)
def buildIdbaStats(infile, outfile):
'''
build idba stats:
N50
Number of scaffolds
Total scaffold length
'''
PipelineGenomeAssembly.contig_to_stats(infile, outfile, PARAMS)
def buildMetavelvetStats(infile, outfile):
'''
build metavelvet stats:
N50
Number of scaffolds
Total scaffold length
'''
PipelineGenomeAssembly.contig_to_stats(infile, outfile, PARAMS)
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 = PipelineGenomeAssembly.Metaphlan().build(infile,
method="rel_ab")
P.run()
def runRay(infile, outfile):
'''
run Ray on each track
'''
to_cluster = True
job_options = " -l mem_free=30G"
statement = PipelineGenomeAssembly.Ray().build(infile)
P.run()
def runMetavelvet(infile, outfile):
'''
run meta-velvet on each track
'''
to_cluster = True
job_options = " -l mem_free=30G"
statement = PipelineGenomeAssembly.Metavelvet().build(infile)
P.run()
def buildContigLengths(infile, outfile):
'''
output lengths for each contig in each of the assemblies
'''
PipelineGenomeAssembly.build_scaffold_lengths(infile, outfile, PARAMS)
def buildContigLengths(infile, outfile):
'''
output lengths for each contig in each of the assemblies
'''
PipelineGenomeAssembly.build_scaffold_lengths(infile, outfile, PARAMS)
