Commit bd606024 authored by Floreal Cabanettes's avatar Floreal Cabanettes
Browse files

Fix set input from res dir for split query + add debug

parent 6ea221dc
...@@ -25,6 +25,7 @@ from dgenies.bin.sort_paf import Sorter ...@@ -25,6 +25,7 @@ from dgenies.bin.sort_paf import Sorter
import gzip import gzip
import io import io
import binascii import binascii
import glob
class JobManager: class JobManager:
...@@ -73,9 +74,11 @@ class JobManager: ...@@ -73,9 +74,11 @@ class JobManager:
if os.path.exists(query_file): if os.path.exists(query_file):
with open(query_file) as q_f: with open(query_file) as q_f:
file_path = q_f.readline() file_path = q_f.readline()
file_path_dir = os.path.dirname(file_path)
split_query = glob.glob(os.path.join(file_path_dir, "split_query_*"))
self.query = Fasta( self.query = Fasta(
name=os.path.splitext(os.path.basename(file_path.replace(".gz", "")).split("_", 1)[1])[0], name=os.path.splitext(os.path.basename(file_path.replace(".gz", "")).split("_", 1)[1])[0],
path=file_path, path=file_path if len(split_query) == 0 else split_query,
type_f="local" type_f="local"
) )
target_file = os.path.join(res_dir, ".target") target_file = os.path.join(res_dir, ".target")
...@@ -325,6 +328,7 @@ class JobManager: ...@@ -325,6 +328,7 @@ class JobManager:
args = ["-t", self.config.nb_threads, self.target.get_path(), self.get_query_split()] args = ["-t", self.config.nb_threads, self.target.get_path(), self.get_query_split()]
else: else:
args = ["-t", self.config.nb_threads, "-X", self.target.get_path(), self.target.get_path()] args = ["-t", self.config.nb_threads, "-X", self.target.get_path(), self.target.get_path()]
print(args)
return self.launch_to_cluster(step="start", return self.launch_to_cluster(step="start",
batch_system_type=batch_system_type, batch_system_type=batch_system_type,
command=self.config.minimap2_cluster_exec, command=self.config.minimap2_cluster_exec,
......
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