1.7.7.1 - bug fixes

1. fix a import bug of 'from scipy import stat, log, inf' issue (issue #132 #315)
2. fix a ZeroDivisionError bug when the estimated coverage is 0 (issue #311)
3. Disentangling failed -> Disentangling unsuccessful to avoid panic (issue #308)
4. fix a bug in parsing options when '-F anonym' is used (issue #319)
5. have max_multiplicity passed to no-slim case
6. minor adjustment

GetOrganelleLib/statistical_func.py

@@ -1,12 +1,21 @@
 try:
-    from scipy import stats, inf, log
+    from scipy import stats
 except ImportError:
     class stats:
         class norm:
             def logpdf(foo1, foo2, foo3):
                 raise ImportError("Failed in 'from scipy import stats, inf, log'!")
     inf = float("inf")
     from math import log
+try:
+    from scipy import inf, log
+except ImportError:
+    try:
+        from numpy import inf, log
+    except ImportError:
+        inf = float("inf")
+        from math import log
+
 from copy import deepcopy
 try:
     import numpy as np

GetOrganelleLib/versions.py

@@ -5,6 +5,16 @@ def get_versions():
 
 
 versions = [
+    {
+        "number": "1.7.7.1",
+        "features": [
+            "1. fix a import bug of 'from scipy import stat, log, inf' issue (issue #132 #315)",
+            "2. fix a ZeroDivisionError bug when the estimated coverage is 0 (issue #311)",
+            "3. Disentangling failed -> Disentangling unsuccessful to avoid panic (issue #308)",
+            "4. fix a bug in parsing options when '-F anonym' is used (issue #319)",
+        ],
+        "time": "2024-04-03 17:05 UTC-5"
+    },
     {
         "number": "1.7.7.0",
         "features": [

Utilities/disentangle_organelle_assembly.py

@@ -317,10 +317,10 @@ def disentangle_circular_assembly(fastg_file, tab_file, prefix, weight_factor, t
     except KeyError as e:
         if str(e).strip("'") == options.mode:
             log_handler.error(options.mode + " not found in " + str(options.tab_file) + "!")
-            log_handler.error("Disentangling failed!")
+            log_handler.error("Disentangling unsuccessful!")
         else:
             log_handler.exception(str(e))
-            log_handler.error("Disentangling failed!")
+            log_handler.error("Disentangling unsuccessful!")
             if not options.acyclic_allowed:
                 log_handler.info("You might try again with '--linear' to export contig(s) "
                                  "instead of circular genome.")
@@ -329,7 +329,7 @@ def disentangle_circular_assembly(fastg_file, tab_file, prefix, weight_factor, t
             log_handler.info("Please open an issue at https://github.com/Kinggerm/GetOrganelle/issues if you find bugs!\n")
     except Exception as e:
         log_handler.exception(str(e))
-        log_handler.error("Disentangling failed!")
+        log_handler.error("Disentangling unsuccessful!")
         if not options.acyclic_allowed:
             log_handler.info("You might try again with '--linear' to export contig(s) "
                              "instead of circular genome.")

Utilities/evaluate_assembly_using_mapping.py

@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#!/usr/bin/env python
 # coding:utf8
 
 from argparse import ArgumentParser
@@ -29,7 +29,7 @@
 
 try:
     # python2 UnicodeDecodeError ±
-    reload(sys)
+    reload(sys) # type: ignore
     sys.setdefaultencoding('utf8')
 except NameError:
     pass

Utilities/fastg_to_gfa.py

@@ -21,7 +21,7 @@ def main():
         if type(2/1) == float:
             fastg = input('Please input gfa file:').strip()
         else:
-            fastg = raw_input('Please input gfa file:').strip()
+            fastg = raw_input('Please input gfa file:').strip() # type: ignore
         PATH_OF_THIS_SCRIPT = os.path.split(os.path.realpath(__file__))[0]
         sys.path.insert(0, os.path.join(PATH_OF_THIS_SCRIPT, ".."))
         from GetOrganelleLib.assembly_parser import Assembly

Utilities/get_annotated_regions_from_gb.py

@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#!/usr/bin/env python
 
 import os
 import time

Utilities/gfa_to_fasta.py

@@ -33,7 +33,7 @@ def main():
         if type(2/1) == float:
             gfa_file = input('Please input gfa file:').strip()
         else:
-            gfa_file = raw_input('Please input gfa file:').strip()
+            gfa_file = raw_input('Please input gfa file:').strip() # type: ignore
         if gfa_file.strip():
             write_fasta(gfa_file +'.fasta', read_gfa_as_fasta(gfa_file), False)
 

Utilities/gfa_to_fastg.py

@@ -21,7 +21,7 @@ def main():
         if type(2/1) == float:
             gfa_file = input('Please input gfa file:').strip()
         else:
-            gfa_file = raw_input('Please input gfa file:').strip()
+            gfa_file = raw_input('Please input gfa file:').strip() # type: ignore
         PATH_OF_THIS_SCRIPT = os.path.split(os.path.realpath(__file__))[0]
         sys.path.insert(0, os.path.join(PATH_OF_THIS_SCRIPT, ".."))
         from GetOrganelleLib.assembly_parser import Assembly

Utilities/join_spades_fastg_by_blast.py

@@ -7,7 +7,7 @@
 import subprocess
 try:
     # python2
-    import commands
+    import commands # type: ignore
 except:
     pass
 from argparse import ArgumentParser

Utilities/rm_low_coverage_duplicated_contigs.py

@@ -3,7 +3,7 @@
 from argparse import ArgumentParser
 import subprocess
 try:
-    import commands
+    import commands # type: ignore
 except:
     pass
 import os

Utilities/round_statistics.py

@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#!/usr/bin/env python
 
 from argparse import ArgumentParser
 import os

Utilities/slim_graph.py

@@ -6,7 +6,7 @@
 import subprocess
 try:
     # python2
-    import commands
+    import commands # type: ignore
 except:
     pass
 inf = float("inf")

get_organelle_from_assembly.py

@@ -396,7 +396,7 @@ def _check_default_db(this_sub_organelle, extra_type=""):
                 log_types.append("embplant_pt")
             log_handler.info("LABEL DB: " + single_line_db_versions(existing_label_db, log_types))
         # working directory
-        log_handler.info("WORKING DIR: " + os.getcwd())
+        log_handler.info("WORKING_DIR=" + os.getcwd())
         log_handler.info(" ".join(["\"" + arg + "\"" if " " in arg else arg for arg in sys.argv]) + "\n")
 
         assert is_valid_path(os.path.realpath(options.output_base)), \
@@ -450,10 +450,13 @@ def _check_default_db(this_sub_organelle, extra_type=""):
                 elif sub_organelle_t in ("embplant_nr", "fungus_nr", "animal_mt"):
                     options.expected_max_size.append(int(raw_default_value / 10))
                 elif sub_organelle_t == "anonym":
-                    ref_seqs = read_fasta(options.genes_fasta[got_t])[1]
-                    options.expected_max_size.append(10 * sum([len(this_seq) for this_seq in ref_seqs]))
-                    log_handler.info("Setting '--expected-max-size " + str(options.expected_max_size) +
-                                     "' for estimating the word size value for anonym type.")
+                    if options.genes_fasta:
+                        ref_seqs = read_fasta(options.genes_fasta[got_t])[1]
+                        options.expected_max_size.append(10 * sum([len(this_seq) for this_seq in ref_seqs]))
+                        log_handler.info("Setting '--expected-max-size " + str(options.expected_max_size) +
+                                        "' for estimating the word size value for anonym type.")
+                    else:
+                        options.expected_max_size.append(inf)
         else:
             temp_val_len = len(str(options.expected_max_size).split(","))
             if temp_val_len != organelle_type_len:
@@ -619,6 +622,7 @@ def disentangle_inside(fastg_f, tab_f, o_p, w_f, log_in, type_f=3., mode_in="emb
             if no_slim:
                 input_graph.estimate_copy_and_depth_by_cov(mode=mode_in, log_handler=log_in, verbose=verbose_in)
                 target_results = input_graph.estimate_copy_and_depth_precisely(
+                    maximum_copy_num=max_copy_in,
                     broken_graph_allowed=acyclic_allowed_in, return_new_graphs=True, verbose=verbose_in,
                     log_handler=log_in)
             else:
@@ -841,11 +845,11 @@ def disentangle_inside(fastg_f, tab_f, o_p, w_f, log_in, type_f=3., mode_in="emb
         if verbose:
             raise e
     except RuntimeError as e:
-        log_handler.info("Disentangling failed: RuntimeError: " + str(e).strip())
+        log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
     except TimeoutError as e:
         log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
     except ProcessingGraphFailed as e:
-        log_handler.info("Disentangling failed: " + str(e).strip())
+        log_handler.info("Disentangling unsuccessful: " + str(e).strip())
     except Exception as e:
         log_handler.exception("")
         raise e
@@ -879,11 +883,11 @@ def disentangle_inside(fastg_f, tab_f, o_p, w_f, log_in, type_f=3., mode_in="emb
             if verbose:
                 raise e
         except RuntimeError as e:
-            log_handler.info("Disentangling failed: RuntimeError: " + str(e).strip())
+            log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
         except TimeoutError as e:
             log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
         except ProcessingGraphFailed as e:
-            log_handler.info("Disentangling failed: " + str(e).strip())
+            log_handler.info("Disentangling unsuccessful: " + str(e).strip())
         except Exception as e:
             log_handler.exception("")
             raise e
@@ -915,11 +919,11 @@ def disentangle_inside(fastg_f, tab_f, o_p, w_f, log_in, type_f=3., mode_in="emb
         except RuntimeError as e:
             if verbose:
                 log_handler.exception("")
-            log_handler.info("Disentangling failed: RuntimeError: " + str(e).strip())
+            log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
         except TimeoutError as e:
             log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
         except ProcessingGraphFailed as e:
-            log_handler.info("Disentangling failed: " + str(e).strip())
+            log_handler.info("Disentangling unsuccessful: " + str(e).strip())
         except Exception as e:
             raise e
         else:

get_organelle_from_reads.py

@@ -716,7 +716,7 @@ def _check_default_db(this_sub_organelle, extra_type=""):
                 log_label_types.append("embplant_pt")
             log_handler.info("LABEL DB: " + single_line_db_versions(existing_label_db, log_label_types))
         # working directory
-        log_handler.info("WORKING DIR: " + os.getcwd())
+        log_handler.info("WORKING_DIR=" + os.getcwd())
         log_handler.info(" ".join(["\"" + arg + "\"" if " " in arg else arg for arg in sys.argv]) + "\n")
 
         # if options.run_spades:
@@ -872,11 +872,14 @@ def _check_default_db(this_sub_organelle, extra_type=""):
                 elif sub_organelle_t in ("embplant_nr", "fungus_nr", "animal_mt"):
                     options.expected_max_size.append(int(raw_default_value / 10))
                 elif sub_organelle_t == "anonym":
-                    ref_seqs = read_fasta(options.genes_fasta[got_t])[1]
-                    options.expected_max_size.append(10 * sum([len(this_seq) for this_seq in ref_seqs]))
-                    log_handler.info(
-                        "Setting '--expected-max-size " + ",".join([str(t_s) for t_s in options.expected_max_size]) +
-                        "' for estimating the word size value for anonym type.")
+                    if options.genes_fasta:
+                        ref_seqs = read_fasta(options.genes_fasta[got_t])[1]
+                        options.expected_max_size.append(10 * sum([len(this_seq) for this_seq in ref_seqs]))
+                        log_handler.info(
+                            "Setting '--expected-max-size " + ",".join([str(t_s) for t_s in options.expected_max_size]) +
+                            "' for estimating the word size value for anonym type.")
+                    else:
+                        options.expected_max_size.append(inf)
         else:
             temp_val_len = len(str(options.expected_max_size).split(","))
             if temp_val_len != organelle_type_len:
@@ -1243,18 +1246,22 @@ def estimate_word_size(base_cov, base_cov_deviation, read_length, target_size, m
         echo_problem = True
     word_cov = max(min_word_cov, word_cov)
     word_cov = trans_word_cov(word_cov, base_cov, mean_error_rate / 2., read_length)
-    # 1. relationship between kmer coverage and base coverage, k_cov = base_cov * (read_len - k_len + 1) / read_len
-    estimated_word_size = int(read_length * (1 - word_cov / base_cov)) + 1
-    # print(estimated_word_size)
-    estimated_word_size = min(int(read_length * MAX_RATIO_RL_WS), max(min_word_size, estimated_word_size))
-    if echo_problem:
-        if log_handler:
-            log_handler.warning("Guessing that you are using too few data for assembling " + organelle_type + "!")
-            log_handler.warning("GetOrganelle is still trying ...")
-        else:
-            sys.stdout.write("Guessing that you are using too few data for assembling " + organelle_type + "!\n")
-            sys.stdout.write("GetOrganelle is still trying ...\n")
-    return int(round(estimated_word_size, 0))
+    if base_cov == 0:
+        log_handler.error("Word size estimation failed due to improper seed or too few input data!")
+        sys.exit()
+    else:
+        # 1. relationship between kmer coverage and base coverage, k_cov = base_cov * (read_len - k_len + 1) / read_len
+        estimated_word_size = int(read_length * (1 - word_cov / base_cov)) + 1
+        # print(estimated_word_size)
+        estimated_word_size = min(int(read_length * MAX_RATIO_RL_WS), max(min_word_size, estimated_word_size))
+        if echo_problem:
+            if log_handler:
+                log_handler.warning("Guessing that you are using too few data for assembling " + organelle_type + "!")
+                log_handler.warning("GetOrganelle is still trying ...")
+            else:
+                sys.stdout.write("Guessing that you are using too few data for assembling " + organelle_type + "!\n")
+                sys.stdout.write("GetOrganelle is still trying ...\n")
+        return int(round(estimated_word_size, 0))
 
 
 def calculate_word_size_according_to_ratio(word_size_ratio, mean_read_len, log_handler):
@@ -3619,11 +3626,11 @@ def disentangle_inside(fastg_f, tab_f, o_p, w_f, log_in, type_f=3., mode_in="emb
             except RuntimeError as e:
                 if verbose:
                     log_handler.exception("")
-                log_handler.info("Disentangling failed: RuntimeError: " + str(e).strip())
+                log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
             except TimeoutError:
                 log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
             except ProcessingGraphFailed as e:
-                log_handler.info("Disentangling failed: " + str(e).strip())
+                log_handler.info("Disentangling unsuccessful: " + str(e).strip())
             except Exception as e:
                 log_handler.exception("")
                 sys.exit()
@@ -3663,11 +3670,11 @@ def disentangle_inside(fastg_f, tab_f, o_p, w_f, log_in, type_f=3., mode_in="emb
                 except RuntimeError as e:
                     if verbose:
                         log_handler.exception("")
-                    log_handler.info("Disentangling failed: RuntimeError: " + str(e).strip())
+                    log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
                 except TimeoutError:
                     log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
                 except ProcessingGraphFailed as e:
-                    log_handler.info("Disentangling failed: " + str(e).strip())
+                    log_handler.info("Disentangling unsuccessful: " + str(e).strip())
                 except Exception as e:
                     log_handler.exception("")
                     sys.exit()
@@ -3708,11 +3715,11 @@ def disentangle_inside(fastg_f, tab_f, o_p, w_f, log_in, type_f=3., mode_in="emb
                     except RuntimeError as e:
                         if verbose:
                             log_handler.exception("")
-                        log_handler.info("Disentangling failed: RuntimeError: " + str(e).strip())
+                        log_handler.info("Disentangling unsuccessful: RuntimeError: " + str(e).strip())
                     except TimeoutError:
                         log_handler.info("Disentangling timeout. (see " + timeout_flag + " for more)")
                     except ProcessingGraphFailed as e:
-                        log_handler.info("Disentangling failed: " + str(e).strip())
+                        log_handler.info("Disentangling unsuccessful: " + str(e).strip())
                     except Exception as e:
                         raise e
                     else: