Commit b362401e authored by Floreal Cabanettes's avatar Floreal Cabanettes
Browse files

If there are too matches for display them in memory, display only the 150.000...

If there are too matches for display them in memory, display only the 150.000 best ones (based on size * identity of matches)
parent 423f09f9
......@@ -10,7 +10,8 @@ fasta_q=$5
query=$6
target=$7
paf=$8
out_dir=$9
paf_raw=$9
out_dir=${10}
# Index fasta files:
${samtools_exec} faidx ${fasta_q}
......@@ -21,18 +22,26 @@ if [ "$fasta_t" != "NONE" ]; then
${samtools_exec} faidx ${fasta_t}
${minimap_exec} -t ${nb_threads} ${fasta_t} ${fasta_q} > ${paf}
echo "Running: ${minimap_exec} -t ${nb_threads} ${fasta_t} ${fasta_q} > ${paf_raw}"
${minimap_exec} -t ${nb_threads} ${fasta_t} ${fasta_q} > ${paf_raw}
# Parse paf raw file:
build_indexes.py -q ${fasta_q} -t ${fasta_t} -o ${out_dir} -r ${query} -u ${target}
else
echo "Running: ${minimap_exec} -t ${nb_threads} -X ${fasta_q} ${fasta_q} > ${paf}"
echo "Running: ${minimap_exec} -t ${nb_threads} -X ${fasta_q} ${fasta_q} > ${paf_raw}"
${minimap_exec} -t ${nb_threads} -X ${fasta_q} ${fasta_q} > ${paf}
${minimap_exec} -t ${nb_threads} -X ${fasta_q} ${fasta_q} > ${paf_raw}
# Parse paf raw file:
build_indexes.py -q ${fasta_q} -t ${fasta_q} -o ${out_dir} -r ${query} -u ${query}
fi
\ No newline at end of file
fi
# Sort PAF file:
sort_paf.py -i ${paf_raw} -o ${paf}
# Remove raw file:
#rm -f ${paf_raw}
\ No newline at end of file
#!/usr/bin/env python3
"""Sort PAF file
Short desc: Sort PAF file with size of matches (DESC)
Details: Sort PAF file with size of matches (DESC)
Usage:
sort_paf.py -i PAF -o OUT
sort_paf.py -v | --version
Options:
-i --input=PAF Input PAF file
-o --output=OUT Output sorted PAF file
-h --help Show this screen
-v --version Show version
"""
import os
from docopt import docopt
from math import sqrt
__NAME__ = "PreparePAF"
__VERSION__ = 0.1
def __sort_key_paf_lines(a):
x1 = int(a[2])
x2 = int(a[3])
y1 = int(a[7])
y2 = int(a[8])
return -sqrt(pow(x2 - x1, 2) + pow(y2 - y1, 2)) * (int(a[9]) / int(a[10]))
def __get_sorted_paf_lines(lines):
paf_lines = []
for line in lines:
parts = line.strip("\n").split("\t")
paf_lines.append(parts)
paf_lines.sort(key=lambda x: __sort_key_paf_lines(x))
return paf_lines
def init(input_f, output_f):
with open(input_f, "r") as paf_file:
paf_lines = paf_file.readlines()
paf_lines = __get_sorted_paf_lines(paf_lines)
with open(output_f, "w") as out:
out.write("\n".join(["\t".join(x) for x in paf_lines]))
if __name__ == '__main__':
args = docopt(__doc__)
if args["--version"]:
print(__NAME__, __VERSION__)
else:
if not os.path.exists(args["--input"]):
raise Exception("Input PAF file %s does not exists" % args["--input"])
init(args["--input"], args["--output"])
\ No newline at end of file
......@@ -298,4 +298,9 @@ footer {
footer hr {
margin-top: 0;
}
/* Notify.js */
.notifyjs-corner {
top: 50px !important;
}
\ No newline at end of file
......@@ -96,6 +96,9 @@ d3.boxplot.launch = function(res, update=false) {
d3.boxplot.events.init();
d3.boxplot.controls.init();
}
if (res["sampled"]) {
dgenies.notify("There are too much matches.\nOnly the 150.000 best matches are displayed")
}
};
d3.boxplot.select_zone = function (x, y) {
......
dgenies = {}
dgenies.notify = function(text) {
$.notify(text, {
className: "warn",
globalPosition: "top",
position: "right",
autoHideDelay: 10000
})
}
\ No newline at end of file
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n=e(this).data(r);n&&n.show(!1)})})})
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......@@ -26,6 +26,7 @@ class JobManager:
# Outputs:
self.output_dir = os.path.join(self.app_data, id_job)
self.paf = os.path.join(self.output_dir, "map.paf")
self.paf_raw = os.path.join(self.output_dir, "map_raw.paf")
self.idx_q = os.path.join(self.output_dir, "query.idx")
self.idx_t = os.path.join(self.output_dir, "target.idx")
self.logs = os.path.join(self.output_dir, "logs.txt")
......@@ -48,7 +49,7 @@ class JobManager:
def __launch_local(self):
cmd = ["run_minimap2.sh", self.minimap2, self.samtools, self.threads,
self.fasta_t if self.fasta_t is not None else "NONE", self.fasta_q, self.query,
self.target, self.paf, self.output_dir]
self.target, self.paf, self.paf_raw, self.output_dir]
with open(self.logs, "w") as logs:
p = subprocess.Popen(cmd, stdout=logs, stderr=logs)
job = Job.get(id_job=self.id_job)
......
#!/usr/bin/env python3
from shutil import copyfile
import os
from math import sqrt
from numpy import mean
......@@ -8,6 +7,7 @@ from numpy import mean
class Paf:
limit_idy = 0.5
max_nb_lines = 150000
def __init__(self, paf: str, idx_q: str, idx_t: str):
self.paf = paf
......@@ -18,6 +18,7 @@ class Paf:
self.paf += ".sorted"
self.idx_q += ".sorted"
self.sorted = True
self.sampled= False
self.len_q = None
self.len_t = None
self.min_idy = None
......@@ -90,7 +91,10 @@ class Paf:
try:
with open(self.paf, "r") as paf_file:
for line in paf_file:
paf_lines = paf_file.readlines()
if len(paf_lines) > self.max_nb_lines:
self.sampled = True
for line in paf_lines[:self.max_nb_lines]:
parts = line.strip("\n").split("\t")
v1 = parts[0]
v6 = parts[5]
......@@ -144,6 +148,7 @@ class Paf:
'name_x': self.name_t,
'limit_idy': self.limit_idy,
'sorted': self.sorted,
'sampled': self.sampled
}
def save_json(self, out):
......
......@@ -4,9 +4,11 @@
<meta charset="UTF-8">
<title>{{ title }}</title>
{% block scripts %}
<script src="{{ url_for('static', filename='js/jquery-3.2.1.min.js') }}" type="text/JavaScript"></script>
<script src="{{ url_for('static', filename='js/popper.min.js') }}" type="text/JavaScript"></script>
<script src="{{ url_for('static', filename='js/bootstrap.min.js') }}" type="text/JavaScript"></script>
<script src="{{ url_for('static', filename='js/jquery-3.2.1.min.js') }}" type="text/JavaScript"></script>
<script src="{{ url_for('static', filename='js/popper.min.js') }}" type="text/JavaScript"></script>
<script src="{{ url_for('static', filename='js/bootstrap.min.js') }}" type="text/JavaScript"></script>
<script src="{{ url_for('static', filename='js/notify.min.js') }}" type="text/JavaScript"></script>
<script src="{{ url_for('static', filename='js/dgenies.js') }}" type="text/JavaScript"></script>
{% endblock %}
<link rel="stylesheet" href="{{ url_for('static', filename='css/jquery-ui.min.css') }}" type="text/css">
<link rel="stylesheet" href="{{ url_for('static', filename='css/bootstrap.min.css') }}" type="text/css">
......
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