def run_blastp(infile, outfile, database, cpus, evalue=1e-10, shell=False):
"""
Query your cluster sequences against an AA database (designed with MIBiG in mind) using blastp.
:param infile: the query cluster AA sequences file (mpfa format)
:param outfile: the resulting blastp output table file
:param database: path to the blast database files, generated with makeblastdb command
:param evalue: the evalue cutoff (default=1e-10)
:param cpus: the number of cpus to use
:param shell: whether to use the shell NOT RECOMMENDED (default=False)
:return: the STDERR/STDOUT
"""
# Deal with any spaces in the file paths
if ' ' in infile:
infile = ''.join(['"', infile, '"'])
if ' ' in outfile:
outfile = ''.join(['"', outfile, '"'])
if ' ' in database:
database = ''.join(['"', database, '"'])
# DEBUG
# print('\n')
# print(infile)
# print(outfile)
# print(database)
cmd = [
'blastp', '-db',
str(database), '-query',
str(infile), '-out',
str(outfile), '-num_threads',
str(cpus), '-outfmt', '6', '-max_hsps', '1', '-evalue', evalue
]
return run_command(cmd, shell=shell)
def run_makeblastdb(infile, outfile, shell=False):
"""
Query your cluster sequences against an AA database (designed with MIBiG in mind) using blastp.
:param infile: the query cluster AA sequences file (mpfa format)
:param outfile: the resulting blastp databsefile
:param shell: whether to use the shell NOT RECOMMENDED (default=False)
:return: the STDERR/STDOUT
"""
# Deal with any spaces in the file paths
if ' ' in infile:
infile = ''.join(['"', infile, '"'])
if ' ' in outfile:
outfile = ''.join(['"', outfile, '"'])
# DEBUG
# print('\n')
# print(infile)
# print(outfile)
# print(database)
cmd = [
'makeblastdb', '-in',
str(infile), '-out',
str(outfile), '-dbtype', 'prot', '-hash_index'
]
# print(cmd)
return run_command(cmd, shell=shell)
def run_shogun(inpath, outpath, utree_db, threads, shell=False):
"""
Run SHOGUN LCA using UTree.
:param input: Directory with the FASTA files, ".fna" extension required
:param output: Output directory for the result files
:param utree_db: path to the UTree database (".ctr" extension
:param threads:
:param cpus: the number of cpus to use
:param shell: whether to use the shell NOT RECOMMENDED (default=False)
:return: the STDERR/STDOUT
"""
# Deal with any spaces in the file paths
if ' ' in inpath:
inpath = ''.join(['"', inpath, '"'])
if ' ' in outpath:
outpath = ''.join(['"', outpath, '"'])
if ' ' in utree_db:
utree_db = ''.join(['"', utree_db, '"'])
cmd = [
'shogun_utree_lca', '-i',
str(inpath), '-o',
str(outpath), '-u',
str(utree_db), '-p',
str(threads)
]
return run_command(cmd, shell=shell)
def bowtie2_align(infile, outfile, database, alignments_to_report=32, num_threads=SETTINGS.N_jobs, shell=False):
"""
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', '0',
'--mp', '"1,1"',
'--rdg', '"0,1"',
'--rfg', '"0,1"',
'--score-min', '"L,0,-0.02"',
'--norc',
'-f', infile,
'--very-sensitive',
'-k', str(alignments_to_report),
'-p', str(num_threads),
'--no-hd']
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)
def utree_search_gg(input_compressed_tree, input_fasta_to_search, output, shell=False):
# usage: xtree-searchGG compTreeGG.ctr fastaToSearch.fa output.txt
cmd = [
'utree-search_gg',
input_compressed_tree,
input_fasta_to_search,
output
]
return run_command(cmd, shell=shell)
def utree_build(input_fasta, input_fasta_labels, output_uncompressed_tree, threads=SETTINGS.N_jobs, 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 bowtie2_build(infile, outfile, offrate=3, 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 offrate: offrate for the index (default=3)
:param shell: whether to use the shell NOT RECOMMENDED (default=False)
:return: teh STDERR/STDOUT
"""
cmd = ['bowtie2-build', '-f', '-o', str(offrate), infile, outfile]
return run_command(cmd, shell=shell)
def embalmer_align(queries, references, outfile, mode='CAPITALIST2', num_threads=SETTINGS.N_jobs, shell=False):
cmd = [
'embalmer',
'--queries', queries,
'--references', references,
'--output', outfile,
'--threads', str(num_threads),
'--mode', mode,
'--shear',
'--latency', 16,
'--id', .985,
]
return run_command(cmd, shell=shell)
def dustmasker(infile, outfile, infmt='fasta', outfmt='fasta', shell=False):
"""
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 = [
'dustmasker',
'-in', infile,
'-out', outfile,
'-infmt', infmt,
'-outfmt', outfmt
]
cmd = [str(i) for i in cmd]
return run_command(cmd, shell=shell)
def run_beta_div(infile,
id_level,
mapping,
variable,
metric,
outdir,
shell=False):
"""
Calculate beta diversity for the matched OFUs and compare between variables of interest from a mapping file.
:param infile: the OFU table at a given cluster ID
:param id_level: the clustering height level (0-100)
:param mapping: the mapping file in standard format (#SampleID is col 1 header)
:param variable: the mapping file header for the variable of interest
:param metric: the distance method to use: manhattan, euclidean, canberra, bray, kulczynski, jaccard, gower, altGower, morisita, horn, mountford, raup , binomial, chao, cao, or mahalanobis.
:param outdir: the output directory/prefix - given as a string that will be appended with the ID and .png file extension
:param shell: whether to use the shell NOT RECOMMENDED (default=False)
:return: the STDERR/STDOUT
"""
# Deal with any spaces in the file paths
if ' ' in infile:
infile = ''.join(['"', infile, '"'])
if ' ' in mapping:
mapping = ''.join(['"', mapping, '"'])
if ' ' in outdir:
outdir = ''.join(['"', outdir, '"'])
# DEBUG
# print('\n')
# print(infile)
# print(outfile)
# print(database)
cmd = [
'ofu_beta_div.R',
str(infile),
str(id_level),
str(mapping),
str(variable),
str(metric),
str(outdir)
]
return run_command(cmd, shell=shell)
def run_alpha_div(infile,
id_level,
mapping,
variable,
metric,
outdir,
shell=False):
"""
Calculate alpha diversity for the matched OFUs and compare between variables of interest from a mapping file.
:param infile: the OFU table at a given cluster ID
:param id_level: the clustering height level (0-100)
:param mapping: the mapping file in standard format (#SampleID is col 1 header)
:param variable: the mapping file header for the variable of interest
:param metric: the diversity metric to use: shannon, simpson, or invsimpson
:param outdir: the output directory/prefix - given as a string that will be appended with the metric, ID level, and .png file extension
:param shell: whether to use the shell NOT RECOMMENDED (default=False)
:return: the STDERR/STDOUT
"""
# Deal with any spaces in the file paths
if ' ' in infile:
infile = ''.join(['"', infile, '"'])
if ' ' in mapping:
mapping = ''.join(['"', mapping, '"'])
if ' ' in outdir:
outdir = ''.join(['"', outdir, '"'])
# DEBUG
# print('\n')
# print(infile)
# print(outfile)
# print(database)
cmd = [
'ofu_beta_div.R',
str(infile),
str(id_level),
str(mapping),
str(variable),
str(metric),
str(outdir)
]
return run_command(cmd, shell=shell)