def rapmap_index(gtf_file, ref_file, algorithm, data, out_dir):
valid_indexes = ["pseudoindex", "quasiindex"]
index_type = algorithm + "index"
assert index_type in valid_indexes, \
"RapMap only supports %s indices." % valid_indexes
out_dir = os.path.join(out_dir, index_type, dd.get_genome_build(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambguate(data))
rapmap = config_utils.get_program("rapmap", dd.get_config(data))
# use user supplied transcriptome FASTA file if it exists
if dd.get_transcriptome_fasta(data):
out_dir = os.path.join(out_dir, index_type, dd.get_genome_build(data))
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
tmpdir = dd.get_tmp_dir(data)
if file_exists(out_dir + "rapidx.jfhash"):
return out_dir
files = dd.get_input_sequence_files(data)
kmersize = sailfish.pick_kmersize(files[0])
message = "Creating rapmap {index_type} for {gtf_fa} with {kmersize} bp kmers."
with file_transaction(out_dir) as tx_out_dir:
cmd = "{rapmap} {index_type} -k {kmersize} -i {tx_out_dir} -t {gtf_fa}"
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def salmon_decoy_index(gtf_file, data, out_dir):
input_dir = os.path.join(dd.get_work_dir(data), "inputs", "transcriptome")
decoy_transcriptome = os.path.join(
input_dir,
sailfish.get_build_string(data) + "-decoy.fa")
out_dir = os.path.join(out_dir, "index", sailfish.get_build_string(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambiguate(data))
salmon = config_utils.get_program("salmon", dd.get_config(data))
num_cores = dd.get_num_cores(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
assert file_exists(gtf_fa), "%s was not found, exiting." % gtf_fa
decoy_sequence_file = get_decoy_sequence_file(data)
decoy_name_file = get_decoy_name_file(data)
gtf_fa = create_decoy_transcriptome(gtf_fa, get_decoy_sequence_file(data),
decoy_transcriptome)
out_file = os.path.join(out_dir, "versionInfo.json")
if file_exists(out_file):
logger.info("Transcriptome index for %s detected, skipping building." %
gtf_fa)
return out_dir
files = dd.get_input_sequence_files(data)
kmersize = sailfish.pick_kmersize(files[0])
with file_transaction(data, out_dir) as tx_out_dir:
cmd = (
"{salmon} index -k {kmersize} -p {num_cores} -i {tx_out_dir} -t {gtf_fa} "
"--decoys {decoy_name_file} ")
message = "Creating decoy-aware Salmon index for {gtf_fa} with {kmersize} bp kmers."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def salmon_index(gtf_file, ref_file, data, out_dir):
out_dir = os.path.join(out_dir, "index", sailfish.get_build_string(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambiguate(data))
salmon = config_utils.get_program("salmon", dd.get_config(data))
num_cores = dd.get_num_cores(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
assert file_exists(gtf_fa), "%s was not found, exiting." % gtf_fa
tmpdir = dd.get_tmp_dir(data)
out_file = os.path.join(out_dir, "versionInfo.json")
if file_exists(out_file):
logger.info("Transcriptome index for %s detected, skipping building." %
gtf_fa)
return out_dir
files = dd.get_input_sequence_files(data)
readlength = bam.fastq.estimate_read_length(files[0])
if readlength % 2 == 0:
readlength -= 1
kmersize = min(readlength, 31)
with file_transaction(data, out_dir) as tx_out_dir:
cmd = "{salmon} index -k {kmersize} -p {num_cores} -i {tx_out_dir} -t {gtf_fa}"
message = "Creating Salmon index for {gtf_fa}."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def rapmap_index(gtf_file, ref_file, algorithm, data, out_dir):
valid_indexes = ["pseudoindex", "quasiindex"]
index_type = algorithm + "index"
assert index_type in valid_indexes, \
"RapMap only supports %s indices." % valid_indexes
out_dir = os.path.join(out_dir, index_type, dd.get_genome_build(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambguate(data))
rapmap = config_utils.get_program("rapmap", dd.get_config(data))
# use user supplied transcriptome FASTA file if it exists
if dd.get_transcriptome_fasta(data):
out_dir = os.path.join(out_dir, index_type, dd.get_genome_build(data))
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
tmpdir = dd.get_tmp_dir(data)
if file_exists(out_dir + "rapidx.jfhash"):
return out_dir
files = dd.get_input_sequence_files(data)
kmersize = sailfish.pick_kmersize(files[0])
message = "Creating rapmap {index_type} for {gtf_fa} with {kmersize} bp kmers."
with file_transaction(out_dir) as tx_out_dir:
cmd = "{rapmap} {index_type} -k {kmersize} -i {tx_out_dir} -t {gtf_fa}"
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def salmon_index(gtf_file, ref_file, data, out_dir):
out_dir = os.path.join(out_dir, "index", sailfish.get_build_string(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambiguate(data))
salmon = config_utils.get_program("salmon", dd.get_config(data))
num_cores = dd.get_num_cores(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data, out_dir)
assert file_exists(gtf_fa), "%s was not found, exiting." % gtf_fa
tmpdir = dd.get_tmp_dir(data)
out_file = os.path.join(out_dir, "versionInfo.json")
if file_exists(out_file):
return out_dir
files = dd.get_input_sequence_files(data)
readlength = bam.fastq.estimate_read_length(files[0])
if readlength % 2 == 0:
readlength -= 1
kmersize = min(readlength, 31)
with file_transaction(data, out_dir) as tx_out_dir:
cmd = "{salmon} index -k {kmersize} -p {num_cores} -i {tx_out_dir} -t {gtf_fa}"
message = "Creating Salmon index for {gtf_fa}."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def use_installed_transcriptome(data):
user_fa = dd.get_transcriptome_fasta(data)
user_gtf = dd.get_transcriptome_gtf(data)
if not user_fa and not user_gtf:
return True
else:
return False
def run_pizzly(data):
work_dir = dd.get_work_dir(data)
pizzlydir = os.path.join(work_dir, "pizzly")
samplename = dd.get_sample_name(data)
gtf = dd.get_gtf_file(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
fraglength = get_fragment_length(data)
cachefile = os.path.join(pizzlydir, "pizzly.cache")
fusions = kallisto.get_kallisto_fusions(data)
pizzlypath = config_utils.get_program("pizzly", dd.get_config(data))
outdir = pizzly(pizzlypath, gtf, gtf_fa, fraglength, cachefile, pizzlydir,
fusions, samplename, data)
return outdir
def run_pizzly(data):
work_dir = dd.get_work_dir(data)
pizzlydir = os.path.join(work_dir, "pizzly")
samplename = dd.get_sample_name(data)
gtf = dd.get_gtf_file(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
fraglength = get_fragment_length(data)
cachefile = os.path.join(pizzlydir, "pizzly.cache")
fusions = kallisto.get_kallisto_fusions(data)
pizzlypath = config_utils.get_program("pizzly", dd.get_config(data))
outdir = pizzly(pizzlypath, gtf, gtf_fa, fraglength, cachefile, pizzlydir,
fusions, samplename, data)
return outdir
def use_installed_transcriptome(data):
user_fa = dd.get_transcriptome_fasta(data)
user_gtf = dd.get_transcriptome_gtf(data)
if not user_fa and not user_gtf:
return True
else:
return False
def salmon_index(gtf_file, ref_file, data, out_dir):
out_dir = os.path.join(out_dir, "index", dd.get_genome_build(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambguate(data))
salmon = config_utils.get_program("salmon", dd.get_config(data))
num_cores = dd.get_num_cores(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data, out_dir)
tmpdir = dd.get_tmp_dir(data)
out_file = os.path.join(out_dir, "versionInfo.json")
if file_exists(out_file):
return out_dir
with file_transaction(out_dir) as tx_out_dir:
cmd = "{salmon} index -k 31 -p {num_cores} -i {tx_out_dir} -t {gtf_fa}"
message = "Creating Salmon index for {gtf_fa}."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def salmon_index(gtf_file, ref_file, data, out_dir):
out_dir = os.path.join(out_dir, "index", dd.get_genome_build(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambguate(data))
salmon = config_utils.get_program("salmon", dd.get_config(data))
num_cores = dd.get_num_cores(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data, out_dir)
tmpdir = dd.get_tmp_dir(data)
out_file = os.path.join(out_dir, "versionInfo.json")
if file_exists(out_file):
return out_dir
with file_transaction(out_dir) as tx_out_dir:
cmd = "{salmon} index -k 31 -p {num_cores} -i {tx_out_dir} -t {gtf_fa}"
message = "Creating Salmon index for {gtf_fa}."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def kallisto_index(gtf_file, ref_file, data, out_dir):
out_dir = os.path.join(out_dir, "index")
out_stem = dd.get_genome_build(data)
if dd.get_disambiguate(data):
out_stem = "-".join([out_stem] + dd.get_disambiguate(data))
index_dir = os.path.join(out_dir, out_stem)
out_file = os.path.join(index_dir, out_stem + ".idx")
kallisto = config_utils.get_program("kallisto", dd.get_config(data))
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
if file_exists(out_file):
return out_file
with file_transaction(out_file) as tx_out_file:
cmd = "{kallisto} index -k 31 -i {tx_out_file} {gtf_fa}"
message = "Creating Kallisto index for {gtf_fa}."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_file
def kallisto_index(gtf_file, ref_file, data, out_dir):
out_dir = os.path.join(out_dir, "index")
out_stem = dd.get_genome_build(data)
if dd.get_disambiguate(data):
out_stem = "-".join([out_stem] + dd.get_disambiguate(data))
index_dir = os.path.join(out_dir, out_stem)
out_file = os.path.join(index_dir, out_stem + ".idx")
kallisto = config_utils.get_program("kallisto", dd.get_config(data))
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
if file_exists(out_file):
return out_file
with file_transaction(out_file) as tx_out_file:
cmd = "{kallisto} index -k 31 -i {tx_out_file} {gtf_fa}"
message = "Creating Kallisto index for {gtf_fa}."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_file
def run_pizzly(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
pizzlydir = os.path.join(work_dir, "pizzly")
gtf = dd.get_transcriptome_gtf(data)
if not gtf:
gtf = dd.get_gtf_file(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
stripped_fa = os.path.splitext(os.path.basename(gtf_fa))[0] + "-noversions.fa"
stripped_fa = os.path.join(pizzlydir, stripped_fa)
gtf_fa = fasta.strip_transcript_versions(gtf_fa, stripped_fa)
fraglength = get_fragment_length(data)
cachefile = os.path.join(pizzlydir, "pizzly.cache")
fusions = kallisto.get_kallisto_fusions(data)
pizzlypath = config_utils.get_program("pizzly", dd.get_config(data))
outdir = pizzly(pizzlypath, gtf, gtf_fa, fraglength, cachefile, pizzlydir,
fusions, samplename, data)
return outdir
def run_pizzly(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
pizzlydir = os.path.join(work_dir, "pizzly")
gtf = dd.get_transcriptome_gtf(data)
if not gtf:
gtf = dd.get_gtf_file(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
stripped_fa = os.path.splitext(
os.path.basename(gtf_fa))[0] + "-noversions.fa"
stripped_fa = os.path.join(pizzlydir, stripped_fa)
gtf_fa = fasta.strip_transcript_versions(gtf_fa, stripped_fa)
fraglength = get_fragment_length(data)
cachefile = os.path.join(pizzlydir, "pizzly.cache")
fusions = kallisto.get_kallisto_fusions(data)
pizzlypath = config_utils.get_program("pizzly", dd.get_config(data))
outdir = pizzly(pizzlypath, gtf, gtf_fa, fraglength, cachefile, pizzlydir,
fusions, samplename, data)
return outdir
def salmon_index(gtf_file, data, out_dir):
out_dir = os.path.join(out_dir, "index", sailfish.get_build_string(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambiguate(data))
salmon = config_utils.get_program("salmon", dd.get_config(data))
num_cores = dd.get_num_cores(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
assert file_exists(gtf_fa), "%s was not found, exiting." % gtf_fa
tmpdir = dd.get_tmp_dir(data)
out_file = os.path.join(out_dir, "versionInfo.json")
if file_exists(out_file):
return out_dir
files = dd.get_input_sequence_files(data)
kmersize = sailfish.pick_kmersize(files[0])
with file_transaction(data, out_dir) as tx_out_dir:
cmd = "{salmon} index --keepDuplicates -k {kmersize} -p {num_cores} -i {tx_out_dir} -t {gtf_fa}"
message = "Creating Salmon index for {gtf_fa} with {kmersize} bp kmers."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def salmon_index(gtf_file, ref_file, data, out_dir):
out_dir = os.path.join(out_dir, "index", sailfish.get_build_string(data))
if dd.get_disambiguate(data):
out_dir = "-".join([out_dir] + dd.get_disambiguate(data))
salmon = config_utils.get_program("salmon", dd.get_config(data))
num_cores = dd.get_num_cores(data)
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
assert file_exists(gtf_fa), "%s was not found, exiting." % gtf_fa
tmpdir = dd.get_tmp_dir(data)
out_file = os.path.join(out_dir, "versionInfo.json")
if file_exists(out_file):
logger.info("Transcriptome index for %s detected, skipping building." % gtf_fa)
return out_dir
files = dd.get_input_sequence_files(data)
kmersize = sailfish.pick_kmersize(files[0])
with file_transaction(data, out_dir) as tx_out_dir:
cmd = "{salmon} index -k {kmersize} -p {num_cores} -i {tx_out_dir} -t {gtf_fa}"
message = "Creating Salmon index for {gtf_fa} with {kmersize} bp kmers."
do.run(cmd.format(**locals()), message.format(**locals()), None)
return out_dir
def salmon_quant_bam(bam_file, salmon_dir, gtf_file, data):
samplename = dd.get_sample_name(data)
quant_dir = salmon_dir
safe_makedir(salmon_dir)
out_file = os.path.join(quant_dir, "quant.sf")
if file_exists(out_file):
return out_file
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
num_cores = dd.get_num_cores(data)
strandedness = dd.get_strandedness(data).lower()
salmon = config_utils.get_program("salmon", dd.get_config(data))
libtype = _libtype_string(bam_file, strandedness)
num_cores = dd.get_num_cores(data)
cmd = ("{salmon} quant {libtype} -p {num_cores} -t {gtf_fa} "
"-o {tx_out_dir} -a {bam_file} ")
cmd += "--numBootstraps 30 "
with file_transaction(data, quant_dir) as tx_out_dir:
message = "Quantifying transcripts in %s with Salmon." % bam_file
do.run(cmd.format(**locals()), message, None)
return out_file
def salmon_quant_bam(bam_file, salmon_dir, gtf_file, ref_file, data):
samplename = dd.get_sample_name(data)
quant_dir = os.path.join(salmon_dir, "quant")
safe_makedir(salmon_dir)
out_file = os.path.join(quant_dir, "quant.sf")
if file_exists(out_file):
return out_file
if dd.get_transcriptome_fasta(data):
gtf_fa = dd.get_transcriptome_fasta(data)
else:
gtf_fa = sailfish.create_combined_fasta(data)
num_cores = dd.get_num_cores(data)
strandedness = dd.get_strandedness(data).lower()
salmon = config_utils.get_program("salmon", dd.get_config(data))
libtype = _libtype_string(bam_file, strandedness)
num_cores = dd.get_num_cores(data)
cmd = ("{salmon} quant {libtype} -p {num_cores} -t {gtf_fa} "
"-o {tx_out_dir} -a {bam_file} ")
cmd += "--numBootstraps 30 "
with file_transaction(data, quant_dir) as tx_out_dir:
message = "Quantifying transcripts in %s with Salmon." % bam_file
do.run(cmd.format(**locals()), message, None)
return out_file