Fix launch on cluster

src/dgenies/bin/filter_contigs.py

@@ -3,7 +3,10 @@
 import os
 import re
 import shutil
-from dgenies.lib.paf import Index
+try:
+    from dgenies.bin.index import Index
+except ModuleNotFoundError:
+    from index import Index
 from Bio import SeqIO
 
 

src/dgenies/bin/build_index.py → src/dgenies/bin/index.py

@@ -5,6 +5,54 @@ import re
 import gzip
 
 
+class Index:
+
+    def __init__(self):
+        pass
+
+    @staticmethod
+    def load(index_file, merge_splits=False):
+        with open(index_file, "r") as idx_q_f:
+            abs_start = {}
+            abs_current_start = 0
+            c_len = 0
+            name = idx_q_f.readline().strip("\n")
+            order = []
+            contigs = {}
+            reversed_c = {}
+            for line in idx_q_f:
+                parts = line.strip("\n").split("\t")
+                id_c = parts[0]
+                is_split = False
+                if merge_splits:
+                    match = re.match(r"(.+)_###_\d+", id_c)
+                    if match is not None:
+                        id_c = match.group(1)
+                        is_split = True
+                len_c = int(parts[1])
+                if len(parts) > 2:
+                    reversed_c[id_c] = parts[2] == "1"
+                else:
+                    reversed_c[id_c] = False
+                if not is_split or (is_split and id_c not in order):
+                    order.append(id_c)
+                    abs_start[id_c] = abs_current_start
+                    contigs[id_c] = len_c
+                else:
+                    contigs[id_c] += len_c
+                c_len += len_c
+                abs_current_start += len_c
+            return name, order, contigs, reversed_c, abs_start, c_len
+
+    @staticmethod
+    def save(index_file, name, contigs, order, reversed_c):
+        with open(index_file, "w") as idx:
+            idx.write(name + "\n")
+            for contig in order:
+                idx.write("\t".join([contig, str(contigs[contig]), "1" if reversed_c[contig] else "0"])
+                          + "\n")
+
+
 def index_file(fasta_path, fasta_name, out, write_fa=None):
     has_header = False
     next_header = False  # True if next line must be a header line

src/dgenies/lib/job_manager.py

@@ -18,7 +18,7 @@ import traceback
 from pathlib import Path
 from urllib import request, parse
 from dgenies.bin.split_fa import Splitter
-from dgenies.bin.build_index import index_file
+from dgenies.bin.index import index_file
 from dgenies.bin.filter_contigs import Filter
 from dgenies.bin.merge_splitted_chrms import Merger
 from dgenies.bin.sort_paf import Sorter

src/dgenies/lib/paf.py

@@ -11,54 +11,7 @@ mpl.use('Agg')
 from matplotlib import pyplot as plt
 import json
 from collections import Counter
-
-
-class Index:
-
-    def __init__(self):
-        pass
-
-    @staticmethod
-    def load(index_file, merge_splits=False):
-        with open(index_file, "r") as idx_q_f:
-            abs_start = {}
-            abs_current_start = 0
-            c_len = 0
-            name = idx_q_f.readline().strip("\n")
-            order = []
-            contigs = {}
-            reversed_c = {}
-            for line in idx_q_f:
-                parts = line.strip("\n").split("\t")
-                id_c = parts[0]
-                is_split = False
-                if merge_splits:
-                    match = re.match(r"(.+)_###_\d+", id_c)
-                    if match is not None:
-                        id_c = match.group(1)
-                        is_split = True
-                len_c = int(parts[1])
-                if len(parts) > 2:
-                    reversed_c[id_c] = parts[2] == "1"
-                else:
-                    reversed_c[id_c] = False
-                if not is_split or (is_split and id_c not in order):
-                    order.append(id_c)
-                    abs_start[id_c] = abs_current_start
-                    contigs[id_c] = len_c
-                else:
-                    contigs[id_c] += len_c
-                c_len += len_c
-                abs_current_start += len_c
-            return name, order, contigs, reversed_c, abs_start, c_len
-
-    @staticmethod
-    def save(index_file, name, contigs, order, reversed_c):
-        with open(index_file, "w") as idx:
-            idx.write(name + "\n")
-            for contig in order:
-                idx.write("\t".join([contig, str(contigs[contig]), "1" if reversed_c[contig] else "0"])
-                          + "\n")
+from dgenies.bin.index import Index
 
 
 class Paf: