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Commit 7be54d96 authored by Haarst, Jan van's avatar Haarst, Jan van
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Run all parts of reas_all.pl separate.

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src/rules/repeats/reas.rules
+ 184
− 19
View file @ 7be54d96
......@@ -18,12 +18,16 @@ __author__ = "Jan van Haarst"
__email__ = "jan.vanhaarst@wur.nl"
# Download and install samtools
# Download and install reas
rule reas_installation:
output: CONFIG["executables"]["reas"] + 'reas_all.pl'
params : dir = strip_path_level(CONFIG['executables']['reas'],2)
output:
reas = CONFIG["executables"]["reas"] + 'reas_all.pl',
dust = CONFIG["executables"]["reas"] + 'dust',
cross_match = CONFIG["executables"]["reas"] + 'cross_match'
params : dir = strip_path_level(CONFIG['executables']['reas'],1)
threads : 12
shell:
"mkdir -p {params.dir};"
"TEMPDIR=`mktemp -d`;"
"cd $TEMPDIR;"
"git clone " +CONFIG["executable_sources"]['reas_URL'] + " && "
......@@ -32,33 +36,194 @@ rule reas_installation:
"cd code && "
"make -j {threads} && "
"make install && "
"mv -v ../bin {params.dir} &&"
"touch {output} && "
"touch {output.reas} && "
"cd - && "
"cd dust && "
"make && make install && "
"touch {output.dust} && "
"cd - && "
"cd cross_match && "
"make manyreads && "
"mv -v cross_match{{,.manyreads}} ../bin && "
"touch {output.cross_match} && "
"mv -v ../bin/* {params.dir} &&"
"cd / && rm -rf $TEMPDIR;"
rule reas:
#rule reas:
# input:
# reads = CONFIG["reads"],
# REAS = rules.reas_installation.output,
# PATH = strip_path_level(CONFIG['executables']['reas'],1)
# output: "consensus.fa"
# message: """Run ReAS on unpaired data"""
# threads: 8
# params:
# options = CONFIG["reas"]["options"]
# shell:
# """
# if conda info --envs | grep '^reas'
# then
# echo "Conda environment exists"
# else
# conda create --use-index-cache --yes --name reas muscle blast;
# fi
# source activate reas
# export PATH=$PATH:{input.PATH}
# {input.REAS} {params.options} -pa {threads} -read {input.reads} -output {output}
# source deactivate;
# """
rule reas_clean_reads:
input:
rules.reas_installation.output,
reads = CONFIG["reads"],
REAS = rules.reas_installation.output,
PATH = strip_path_level(CONFIG['executables']['reas'],1)
output: "consensus.fa"
message: """Run ReAS on unpaired data"""
output: CONFIG["reas"]["options"]["clean_read_file"]
params:
seqsize = CONFIG["reas"]["options"]["seqsize"]
shell:
"""
export PATH=$PATH:{input.PATH}
cat {input.reads} | CleanData.pl -size={params.seqsize} | rename.pl > {output}
# remove output if empty, or touch if not
[ -s {output} ] && touch {output} || rm -f {output}
"""
rule reas_kmers:
input:
rules.reas_installation.output,
clean_read_file = rules.reas_clean_reads.output,
PATH = strip_path_level(CONFIG['executables']['reas'],1)
output: CONFIG["reas"]["options"]["nmers_file"]
params:
k = CONFIG["reas"]["options"]["k"],
d = CONFIG["reas"]["options"]["d"],
m = CONFIG["reas"]["options"]["m"]
shell:
"""
export PATH=$PATH:{input.PATH}
kmer_num -k {params.k} {input.clean_read_file} | kmer2reads -d {params.d} {input.clean_read_file} | N_mers -m {params.m} > {output}
# remove output if empty, or touch if not
[ -s {output} ] && touch {output} || rm -f {output}
"""
rule reas_subsample:
input:
rules.reas_installation.output,
nmers_file = rules.reas_kmers.output,
PATH = strip_path_level(CONFIG['executables']['reas'],1)
output: CONFIG["reas"]["options"]["hd_read_id_file"]
params:
fraction = CONFIG["reas"]["options"]["fraction"]
shell:
"""
export PATH=$PATH:{input.PATH}
cat {input.nmers_file} | cut -f1 | RandomList.pl {params.fraction} > {output}
# remove output if empty, or touch if not
[ -s {output} ] && touch {output} || rm -f {output}
"""
rule reas_picklist:
input:
rules.reas_installation.output,
clean_read_file = rules.reas_clean_reads.output,
hd_read_id_file = rules.reas_subsample.output,
PATH = strip_path_level(CONFIG['executables']['reas'],1)
output: CONFIG["reas"]["options"]["hd_read_file"]
shell:
"""
export PATH=$PATH:{input.PATH}
cat {input.clean_read_file} | pickListSeq.pl {input.hd_read_id_file} > {output}
# remove output if empty, or touch if not
[ -s {output} ] && touch {output} || rm -f {output}
"""
rule reas_pairwise_alignment:
input:
rules.reas_installation.output,
hd_read_file = rules.reas_picklist.output,
PATH = strip_path_level(CONFIG['executables']['reas'],1)
output: CONFIG["reas"]["options"]["bound_file"]
params:
n = CONFIG["reas"]["options"]["n"],
pa = CONFIG["reas"]["options"]["pa"],
bound_file = CONFIG["reas"]["options"]["bound_file"],
size = CONFIG["reas"]["options"]["size"],
ident = CONFIG["reas"]["options"]["ident"],
d = CONFIG["reas"]["options"]["d"],
t = CONFIG["reas"]["options"]["t"]
threads: 8
shell:
"""
export PATH=$PATH:{input.PATH}
run_HighDseg.pl -r {input.hd_read_file} -n {params.n} -a {threads} -b {output} -s {params.size} -i {params.ident} -d {params.d} -t {params.t}
# remove output if empty, or touch if not
[ -s {output} ] && touch {output} || rm -f {output}
"""
rule reas_cut_segments:
input:
rules.reas_installation.output,
hd_read_file = rules.reas_subsample.output,
bound_file = rules.reas_pairwise_alignment.output,
PATH = strip_path_level(CONFIG['executables']['reas'],1)
output: CONFIG["reas"]["options"]["seg_file"]
params:
n = CONFIG["reas"]["options"]["n"],
pa = CONFIG["reas"]["options"]["pa"],
bound_file = CONFIG["reas"]["options"]["bound_file"],
size = CONFIG["reas"]["options"]["size"],
ident = CONFIG["reas"]["options"]["ident"],
d = CONFIG["reas"]["options"]["d"]
shell:
"""
export PATH=$PATH:{input.PATH}
cat {input.bound_file} | cutSeg.pl {input.hd_read_file} > {output}
# remove output if empty, or touch if not
[ -s {output} ] && touch {output} || rm -f {output}
"""
rule reas_segment_linkage:
input:
rules.reas_installation.output,
hd_read_file = rules.reas_subsample.output,
PATH = strip_path_level(CONFIG['executables']['reas'],1)
output: CONFIG["reas"]["options"]["link_file"]
params:
n = CONFIG["reas"]["options"]["n"],
pa = CONFIG["reas"]["options"]["pa"],
size = CONFIG["reas"]["options"]["size"],
ident = CONFIG["reas"]["options"]["ident"],
nonlcs = CONFIG["reas"]["options"]["nonlcs"]
shell:
"""
export PATH=$PATH:{input.PATH}
run_SegLink.pl -r {input.hd_read_file} -n {params.n} -a {params.pa} {params.size} {params.ident} {params.nonlcs} -o {output}
# remove output if empty, or touch if not
[ -s {output} ] && touch {output} || rm -f {output}
"""
rule reas_repeat_assembly:
input:
rules.reas_installation.output,
seg_file = rules.reas_cut_segments.output,
link_file = rules.reas_segment_linkage.output,
bound_file = rules.reas_pairwise_alignment.output,
PATH = strip_path_level(CONFIG['executables']['reas'],1)
output: CONFIG["reas"]["options"]["output"]
params:
options = CONFIG["reas"]["options"]
sub_multi = CONFIG["reas"]["options"]["sub_multi"],
d = CONFIG["reas"]["options"]["d"],
prefix = CONFIG["reas"]["options"]["prefix"],
log = CONFIG["reas"]["options"]["log"],
end = CONFIG["reas"]["options"]["end"],
min_depth = CONFIG["reas"]["options"]["min_depth"],
min_extend = CONFIG["reas"]["options"]["min_extend"],
max_extend = CONFIG["reas"]["options"]["max_extend"]
shell:
"""
if conda info --envs | grep '^reas'
then
echo "Conda environment exists"
else
conda create --use-index-cache --yes --name reas muscle blast;
fi
source activate reas
export PATH=$PATH:{input.PATH}
{input.REAS} {params.options} -pa {threads} -read {input.reads} -output {output}
source deactivate;
DoAssembly -r {input.seg_file} -l {input.link_file} {params.sub_multi} -b {input.bound_file} -d {params.d} -o {output} {params.prefix} {params.log} -e {params.end} {params.min_depth} {params.min_extend} {params.max_extend}
# remove output if empty, or touch if not
[ -s {output} ] && touch {output} || rm -f {output}
"""
src/workflows/repeats/reas/config.json
+ 28
− 1
View file @ 7be54d96
......@@ -19,7 +19,34 @@
"sra_id" : "ERR171441",
"reas":
{
"options": "--seqsize=80"
"options": {
"k": "17",
"d": "6",
"m": "1",
"fraction": "1",
"n": "1",
"t": "0",
"pa": "1",
"bound_file": "seg.bk",
"link_file": "seg.link",
"sub_multi": "-t -1",
"output": "consensus.fa",
"prefix": "-p ''",
"log": "",
"size": "100",
"seqsize": "80",
"ident": "0.6",
"nonlcs": "50",
"end": "50",
"min_depth": "-j 2",
"min_extend": "-u 50",
"max_extend": "-v 200",
"clean_read_file" : "reads.clean.fa",
"nmers_file" : "read.N_mers",
"hd_read_id_file" : "HD_reads.id",
"hd_read_file" : "HD_reads.fa",
"seg_file" : "seg.fa"
}
},
"sra":
{
......
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