def burst_build(infile,
outfile_prefix,
accelerator=False,
shell=False,
clustradius=None,
shear=None):
cmd = [
'burst15',
'--references',
infile,
'--output',
outfile_prefix + ".edb",
'--npenalize',
'--makedb',
'--fingerprint',
]
if accelerator:
cmd += ['--accelerator', accelerator]
if shear:
cmd += ['--shear', str(shear)]
if clustradius:
cmd += ['--clustradius', str(clustradius)]
return run_command(cmd, shell=shell)
def burst_align_any(input_fp,
output_fp,
burst_db_prefix,
accelerator=False,
threads=1,
shell=False,
percent_id=.98):
"""
:param input_fp:
:param output_fp:
:param burst_db_prefix:
:param accelerator:
:param tax:
:param threads:
:param pct_id:
:param shell:
:param taxa_ncbi:
:return:
"""
#TODO: Look up SOP
cmd = [
'burst15', '--queries', input_fp, '--references',
burst_db_prefix + '.edx', '--output', output_fp, '--threads',
str(threads), '--mode', 'ANY', '--npenalize', '--id',
str(percent_id), '--forwardreverse'
]
if accelerator:
cmd += ['--accelerator', accelerator]
return run_command(cmd, shell=shell)
def bowtie2_align(infile,
outfile,
database,
alignments_to_report=16,
num_threads=1,
shell=False,
percent_id=.98):
"""
Search a bowtie2 index with multiple alignment.
:param infile: the query FASTA file
:param outfile: the resulting SAM file
:param database: path to the bowtie2 index
:param alignments_to_report: the number of alignments to report (default=32)
:param num_threads: the number of threads to use (default=SETTINGS)
:param shell: whether to use the shell NOT RECOMMENDED (default=False)
:return: the STDERR/STDOUT
"""
cmd = [
'bowtie2', '--no-unal', '-x', database, '-S', outfile, '--np', '1',
'--mp', '"1,1"', '--rdg', '"0,1"', '--rfg', '"0,1"', '--score-min',
format_pct_id(percent_id), '-f', infile, '--very-sensitive', '-k',
str(alignments_to_report), '-p',
str(num_threads), '--no-hd'
]
return run_command(cmd, shell=shell)
def utree_search(input_compressed_tree,
input_fasta_to_search,
output,
shell=False):
# usage: xtree-search compTree.ctr fastaToSearch.fa output.txt
cmd = [
'utree-search', input_compressed_tree, input_fasta_to_search, output
]
return run_command(cmd, shell=shell)
def bowtie2_build(infile, outfile, shell=False):
"""
This function will build a bowtie2 index with a given infile and output to the outfile
:param infile: the FASTA file to build the index with
:param outfile: the prefix for the bowtie2 index
:param shell: whether to use the shell NOT RECOMMENDED (default=False)
:return: the STDERR/STDOUT
"""
cmd = ['bowtie2-build', '-f', infile, outfile]
return run_command(cmd, shell=shell)
def utree_search_gg(input_compressed_tree,
input_fasta_to_search,
output,
threads=1,
shell=False):
# [v1.5a] usage: xtree-searchGG compTree.ctr fastaToSearch.fa output.txt [threads] [RC]
cmd = [
'utree-search_gg', input_compressed_tree, input_fasta_to_search,
output, threads, 'RC'
]
return run_command(cmd, shell=shell)
def utree_build_gg(input_fasta,
input_fasta_labels,
output_uncompressed_tree,
threads=1,
complevel=2,
shell=False):
# [v2.0 SigNature Edition] usage: utree-buildGG input_fasta.fa labels.map output.ubt threads{0=auto} [complevel]
cmd = [
'utree-build_gg', input_fasta, input_fasta_labels,
output_uncompressed_tree, threads, complevel
]
return run_command(cmd, shell=shell)
def utree_build(input_fasta,
input_fasta_labels,
output_uncompressed_tree,
threads=1,
shell=False):
# usage: utree-build input_fasta.fa labels.map output.ubt [threads]
cmd = [
'utree-build',
input_fasta,
input_fasta_labels,
output_uncompressed_tree,
threads,
]
return run_command(cmd, shell=shell)
def burst_align(input_fp,
output_fp,
burst_db_prefix,
threads=1,
percent_id=.98,
tax=False,
accelerator=False,
taxacut=5,
shell=False,
taxa_ncbi=False):
"""
:param input_fp:
:param output_fp:
:param burst_db_prefix:
:param accelerator:
:param tax:
:param threads:
:param pct_id:
:param shell:
:param taxa_ncbi:
:return:
"""
#TODO: Look up SOP
cmd = [
'burst15', '--queries', input_fp, '--references',
burst_db_prefix + '.edx', '--output', output_fp, '--threads',
str(threads), '--mode', 'CAPITALIST', '--id',
str(percent_id), '--npenalize', '--skipambig', '--forwardreverse'
]
if taxa_ncbi:
cmd += ['--taxa_ncbi']
if accelerator:
cmd += ['--accelerator', accelerator]
if tax:
cmd += ['--taxonomy', tax, '--taxacut', taxacut]
return run_command(cmd, shell=shell)
def utree_compress(input_uncompressed_tree,
output_compressed_tree,
shell=False):
# usage: xtree-compress preTree.ubt compTree.ctr
cmd = ['utree-compress', input_uncompressed_tree, output_compressed_tree]
return run_command(cmd, shell=shell)