update

DessimozLab · Mar 27, 2023 · b9fc3d7 · b9fc3d7
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diff --git a/FastOMA/__init__.py b/FastOMA/__init__.py
@@ -0,0 +1,3 @@
+
+__packagename__ = "FastOMA"
+__version__ = "0.0.5"
diff --git a/fastoma/_config.py → FastOMA/_config.py b/fastoma/_config.py → FastOMA/_config.py
diff --git a/fastoma/_hog_class.py → FastOMA/_hog_class.py b/fastoma/_hog_class.py → FastOMA/_hog_class.py
diff --git a/fastoma/_infer_subhog.py → FastOMA/_infer_subhog.py b/fastoma/_infer_subhog.py → FastOMA/_infer_subhog.py
diff --git a/fastoma/_utils_roothog.py → FastOMA/_utils_roothog.py b/fastoma/_utils_roothog.py → FastOMA/_utils_roothog.py
diff --git a/fastoma/_utils_subhog.py → FastOMA/_utils_subhog.py b/fastoma/_utils_subhog.py → FastOMA/_utils_subhog.py
diff --git a/fastoma/_wrappers.py → FastOMA/_wrappers.py b/fastoma/_wrappers.py → FastOMA/_wrappers.py
@@ -1,12 +1,13 @@
 
 from Bio import SeqIO
-from fastoma.zoo.wrappers.aligners import mafft
+from FastOMA.zoo.wrappers.aligners import mafft
 # iqtree
-from fastoma.zoo.wrappers.treebuilders import fasttree
+from FastOMA.zoo.wrappers.treebuilders import fasttree
 # from trimmers.trimal import TrimAl
 from ete3 import Tree
 
 
+
 from ._utils_subhog import logger_hog
 from . import _config
 

diff --git a/fastoma/batch_roothogs.py → FastOMA/batch_roothogs.py b/fastoma/batch_roothogs.py → FastOMA/batch_roothogs.py
@@ -7,6 +7,7 @@
 from os import listdir
 from . import _config
 
+
 def list_rhog_fastas(address_rhogs_folder):
     """
      create orthoxml_to_newick.py list of rootHOG IDs  stored in the folder of rHOG .

diff --git a/fastoma/collect_subhogs.py → FastOMA/collect_subhogs.py b/fastoma/collect_subhogs.py → FastOMA/collect_subhogs.py
@@ -22,7 +22,7 @@ def collect_subhogs():
 
     # in_folder = _config.in_folder
 
-    # python ${fastoma} / collect_subhogs.py ${pickle_rhogs} ${gene_id_dic_xml}
+    # python ${FastOMA} / collect_subhogs.py ${pickle_rhogs} ${gene_id_dic_xml}
 
 
     if qfo_bird == "bird_hog":

diff --git a/fastoma/infer_roothogs.py → FastOMA/infer_roothogs.py b/fastoma/infer_roothogs.py → FastOMA/infer_roothogs.py
diff --git a/fastoma/infer_subhogs.py → FastOMA/infer_subhogs.py b/fastoma/infer_subhogs.py → FastOMA/infer_subhogs.py
@@ -11,6 +11,7 @@
 # import _config
 
 
+
 # from ._utils import logger_hog
 # import ._utils_rhog
 

diff --git a/fastoma/requirements → FastOMA/requirements b/fastoma/requirements → FastOMA/requirements
diff --git a/fastoma/zoo/README.md → FastOMA/zoo/README.md b/fastoma/zoo/README.md → FastOMA/zoo/README.md
diff --git a/fastoma/zoo/__init__.py → FastOMA/zoo/__init__.py b/fastoma/zoo/__init__.py → FastOMA/zoo/__init__.py
diff --git a/fastoma/zoo/file_utils/__init__.py → FastOMA/zoo/file_utils/__init__.py b/fastoma/zoo/file_utils/__init__.py → FastOMA/zoo/file_utils/__init__.py
diff --git a/fastoma/zoo/file_utils/context_managers.py → FastOMA/zoo/file_utils/context_managers.py b/fastoma/zoo/file_utils/context_managers.py → FastOMA/zoo/file_utils/context_managers.py
diff --git a/fastoma/zoo/file_utils/extractors.py → FastOMA/zoo/file_utils/extractors.py b/fastoma/zoo/file_utils/extractors.py → FastOMA/zoo/file_utils/extractors.py
diff --git a/fastoma/zoo/hog/__init__.py → FastOMA/zoo/hog/__init__.py b/fastoma/zoo/hog/__init__.py → FastOMA/zoo/hog/__init__.py
diff --git a/fastoma/zoo/hog/convert.py → FastOMA/zoo/hog/convert.py b/fastoma/zoo/hog/convert.py → FastOMA/zoo/hog/convert.py
diff --git a/fastoma/zoo/hog/extract_groups.py → FastOMA/zoo/hog/extract_groups.py b/fastoma/zoo/hog/extract_groups.py → FastOMA/zoo/hog/extract_groups.py
diff --git a/fastoma/zoo/hog/extract_hog_info.py → FastOMA/zoo/hog/extract_hog_info.py b/fastoma/zoo/hog/extract_hog_info.py → FastOMA/zoo/hog/extract_hog_info.py
diff --git a/fastoma/zoo/hog/filter_orthoxml.py → FastOMA/zoo/hog/filter_orthoxml.py b/fastoma/zoo/hog/filter_orthoxml.py → FastOMA/zoo/hog/filter_orthoxml.py
diff --git a/fastoma/zoo/hog/orthoxml_merge.py → FastOMA/zoo/hog/orthoxml_merge.py b/fastoma/zoo/hog/orthoxml_merge.py → FastOMA/zoo/hog/orthoxml_merge.py
diff --git a/fastoma/zoo/seq_utils/__init__.py → FastOMA/zoo/seq_utils/__init__.py b/fastoma/zoo/seq_utils/__init__.py → FastOMA/zoo/seq_utils/__init__.py
diff --git a/fastoma/zoo/seq_utils/utils.py → FastOMA/zoo/seq_utils/utils.py b/fastoma/zoo/seq_utils/utils.py → FastOMA/zoo/seq_utils/utils.py
diff --git a/fastoma/zoo/wrappers/__init__.py → FastOMA/zoo/wrappers/__init__.py b/fastoma/zoo/wrappers/__init__.py → FastOMA/zoo/wrappers/__init__.py
diff --git a/fastoma/zoo/wrappers/abstract_cli.py → FastOMA/zoo/wrappers/abstract_cli.py b/fastoma/zoo/wrappers/abstract_cli.py → FastOMA/zoo/wrappers/abstract_cli.py
diff --git a/fastoma/zoo/wrappers/aligners/__init__.py → FastOMA/zoo/wrappers/aligners/__init__.py b/fastoma/zoo/wrappers/aligners/__init__.py → FastOMA/zoo/wrappers/aligners/__init__.py
diff --git a/...oma/zoo/wrappers/aligners/base_aligner.py → ...OMA/zoo/wrappers/aligners/base_aligner.py b/...oma/zoo/wrappers/aligners/base_aligner.py → ...OMA/zoo/wrappers/aligners/base_aligner.py
diff --git a/fastoma/zoo/wrappers/aligners/mafft.py → FastOMA/zoo/wrappers/aligners/mafft.py b/fastoma/zoo/wrappers/aligners/mafft.py → FastOMA/zoo/wrappers/aligners/mafft.py
diff --git a/fastoma/zoo/wrappers/aligners/muscle.py → FastOMA/zoo/wrappers/aligners/muscle.py b/fastoma/zoo/wrappers/aligners/muscle.py → FastOMA/zoo/wrappers/aligners/muscle.py
diff --git a/fastoma/zoo/wrappers/aligners/probcons.py → FastOMA/zoo/wrappers/aligners/probcons.py b/fastoma/zoo/wrappers/aligners/probcons.py → FastOMA/zoo/wrappers/aligners/probcons.py
diff --git a/fastoma/zoo/wrappers/aligners/prographmsa.py → FastOMA/zoo/wrappers/aligners/prographmsa.py b/fastoma/zoo/wrappers/aligners/prographmsa.py → FastOMA/zoo/wrappers/aligners/prographmsa.py
diff --git a/...oma/zoo/wrappers/modeltesters/__init__.py → ...OMA/zoo/wrappers/modeltesters/__init__.py b/...oma/zoo/wrappers/modeltesters/__init__.py → ...OMA/zoo/wrappers/modeltesters/__init__.py
diff --git a/...wrappers/modeltesters/base_modeltester.py → ...wrappers/modeltesters/base_modeltester.py b/...wrappers/modeltesters/base_modeltester.py → ...wrappers/modeltesters/base_modeltester.py
diff --git a/fastoma/zoo/wrappers/modeltesters/parsers.py → FastOMA/zoo/wrappers/modeltesters/parsers.py b/fastoma/zoo/wrappers/modeltesters/parsers.py → FastOMA/zoo/wrappers/modeltesters/parsers.py
diff --git a/...oma/zoo/wrappers/modeltesters/prottest.py → ...OMA/zoo/wrappers/modeltesters/prottest.py b/...oma/zoo/wrappers/modeltesters/prottest.py → ...OMA/zoo/wrappers/modeltesters/prottest.py
diff --git a/fastoma/zoo/wrappers/options.py → FastOMA/zoo/wrappers/options.py b/fastoma/zoo/wrappers/options.py → FastOMA/zoo/wrappers/options.py
diff --git a/...oma/zoo/wrappers/treebuilders/__init__.py → ...OMA/zoo/wrappers/treebuilders/__init__.py b/...oma/zoo/wrappers/treebuilders/__init__.py → ...OMA/zoo/wrappers/treebuilders/__init__.py
diff --git a/...wrappers/treebuilders/base_treebuilder.py → ...wrappers/treebuilders/base_treebuilder.py b/...wrappers/treebuilders/base_treebuilder.py → ...wrappers/treebuilders/base_treebuilder.py
@@ -7,8 +7,8 @@
 
 
 
-from fastoma.zoo.wrappers import WrapperError
-from fastoma.zoo.wrappers.aligners.base_aligner import identify_input
+from FastOMA.zoo.wrappers import WrapperError
+from FastOMA.zoo.wrappers.aligners.base_aligner import identify_input
 
 import logging
 logger = logging.getLogger(__name__)

diff --git a/...oma/zoo/wrappers/treebuilders/fasttree.py → ...OMA/zoo/wrappers/treebuilders/fasttree.py b/...oma/zoo/wrappers/treebuilders/fasttree.py → ...OMA/zoo/wrappers/treebuilders/fasttree.py
diff --git a/fastoma/zoo/wrappers/treebuilders/guenomu.py → FastOMA/zoo/wrappers/treebuilders/guenomu.py b/fastoma/zoo/wrappers/treebuilders/guenomu.py → FastOMA/zoo/wrappers/treebuilders/guenomu.py
@@ -5,7 +5,7 @@
 import shutil
 from Bio import AlignIO, SeqIO
 import dendropy
-from fastoma.zoo.wrappers import WrapperError
+from FastOMA.zoo.wrappers import WrapperError
 import logging
 
 

diff --git a/fastoma/zoo/wrappers/treebuilders/iqtree.py → FastOMA/zoo/wrappers/treebuilders/iqtree.py b/fastoma/zoo/wrappers/treebuilders/iqtree.py → FastOMA/zoo/wrappers/treebuilders/iqtree.py
diff --git a/fastoma/zoo/wrappers/treebuilders/parsers.py → FastOMA/zoo/wrappers/treebuilders/parsers.py b/fastoma/zoo/wrappers/treebuilders/parsers.py → FastOMA/zoo/wrappers/treebuilders/parsers.py
diff --git a/fastoma/zoo/wrappers/treebuilders/phyml.py → FastOMA/zoo/wrappers/treebuilders/phyml.py b/fastoma/zoo/wrappers/treebuilders/phyml.py → FastOMA/zoo/wrappers/treebuilders/phyml.py
diff --git a/fastoma/zoo/wrappers/treebuilders/raxml.py → FastOMA/zoo/wrappers/treebuilders/raxml.py b/fastoma/zoo/wrappers/treebuilders/raxml.py → FastOMA/zoo/wrappers/treebuilders/raxml.py
diff --git a/fastoma/zoo/wrappers/trimmers/__init__.py → FastOMA/zoo/wrappers/trimmers/__init__.py b/fastoma/zoo/wrappers/trimmers/__init__.py → FastOMA/zoo/wrappers/trimmers/__init__.py
diff --git a/...oma/zoo/wrappers/trimmers/base_trimmer.py → ...OMA/zoo/wrappers/trimmers/base_trimmer.py b/...oma/zoo/wrappers/trimmers/base_trimmer.py → ...OMA/zoo/wrappers/trimmers/base_trimmer.py
diff --git a/fastoma/zoo/wrappers/trimmers/trimal.py → FastOMA/zoo/wrappers/trimmers/trimal.py b/fastoma/zoo/wrappers/trimmers/trimal.py → FastOMA/zoo/wrappers/trimmers/trimal.py
diff --git a/archive/analysis/fastoma_mid_diff.py b/archive/analysis/fastoma_mid_diff.py
@@ -1,5 +1,5 @@
 
-
+import pickle
 
 def prepare_species_tree(rhog_i, species_tree):
     for rec in rhog_i:
@@ -250,7 +250,7 @@ def distribute_rhogs(rhogs: List[Tuple[str, int]], start_index: int, n_workers:
     logger_hog = logging.getLogger("hog")
     logger_hog.setLevel(logging.INFO)  # WARN
     # make sure addresses end with "/"
-    address_working_folder = "/work/FAC/FBM/DBC/cdessim2/default/ayazdiza/fastoma-dask/"
+    address_working_folder = "/work/FAC/FBM/DBC/cdessim2/default/ayazdiza/FastOMA-dask/"
     address_rhogs_folder = "/work/FAC/FBM/DBC/cdessim2/default/ayazdiza/family-score-adjusted/AdjustedFamilyScore_All_rHOGs/"
     address_pickles_folder = "/work/FAC/FBM/DBC/cdessim2/default/ayazdiza/fastoma_repo/temp_results/pickles/mid_adjustedfamily_40_1/"
     species_tree_address = address_working_folder + "lineage_tree_qfo.phyloxml"
@@ -267,6 +267,7 @@ def distribute_rhogs(rhogs: List[Tuple[str, int]], start_index: int, n_workers:
     rhog_files = listdir(address_rhogs_folder)[:]
     print("#", rhog_files, len(rhog_files))
 
+
     file_sizes = [os.path.getsize(f'{address_rhogs_folder}{i}') for i in rhog_files]
     file_name_size_dict = dict(zip(rhog_files, file_sizes))
     file_name_size_list_sorted = sorted(file_name_size_dict.items(), key=lambda x: x[1])

diff --git a/archive/analysis/fastoma_mid_newrhg.py b/archive/analysis/fastoma_mid_newrhg.py
@@ -1,5 +1,5 @@
 
-import dill as pickle
+# import dill as pickle
 import logging
 from datetime import datetime
 from os import listdir
@@ -8,6 +8,7 @@
 from typing import Tuple, List
 from random import sample
 
+
 from ete3 import Phyloxml
 from ete3 import PhyloTree
 

diff --git a/archive/analysis/filter_rhog.py b/archive/analysis/filter_rhog.py
@@ -21,7 +21,7 @@
     file_folders = (address_rhogs_folder, gene_trees_folder, pickle_folder, species_tree_address)
 
 
-    oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/fastoma/archive/OmaServer.h5"
+    oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/FastOMA/archive/OmaServer.h5"
     # in_folder+"omamer_database/oma_path/OmaServer.h5"
     print("rHOG inferece has started. The oma database address is in ", oma_database_address)
     (oma_db, list_oma_species) = _utils_rhog.parse_oma_db(oma_database_address)

diff --git a/archive/analysis/graveyard.py b/archive/analysis/graveyard.py
@@ -551,7 +551,7 @@ def gene_num_convertor_old(rhogid_num_list_input, address_rhogs_folder, format_p
 # import _inferhog
 #
 # # from _utils import logger_hog
-# import fastoma._utils_rhog as _utils_rhog
+# import FastOMA._utils_rhog as _utils_rhog
 #
 # # from distributed import get_client
 # # from dask.distributed import rejoin, secede
@@ -565,7 +565,7 @@ def gene_num_convertor_old(rhogid_num_list_input, address_rhogs_folder, format_p
 #     file_folders = (address_rhogs_folder, gene_trees_folder, pickle_folder, species_tree_address)
 #
 #
-#     oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/fastoma/archive/OmaServer.h5"
+#     oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/FastOMA/archive/OmaServer.h5"
 #     # in_folder+"omamer_database/oma_path/OmaServer.h5"
 #     print("rHOG inferece has started. The oma database address is in ", oma_database_address)
 #     (oma_db, list_oma_species) = _utils_rhog.parse_oma_db(oma_database_address)
@@ -1162,7 +1162,7 @@ def gene_num_convertor_old(rhogid_num_list_input, address_rhogs_folder, format_p
 # import _inferhog
 #
 # # from _utils import logger_hog
-# import fastoma._utils_rhog as _utils_rhog
+# import FastOMA._utils_rhog as _utils_rhog
 #
 # # from distributed import get_client
 # # from dask.distributed import rejoin, secede
@@ -1176,7 +1176,7 @@ def gene_num_convertor_old(rhogid_num_list_input, address_rhogs_folder, format_p
 #     file_folders = (address_rhogs_folder, gene_trees_folder, pickle_folder, species_tree_address)
 #
 #
-#     oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/fastoma/archive/OmaServer.h5"
+#     oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/FastOMA/archive/OmaServer.h5"
 #     # in_folder+"omamer_database/oma_path/OmaServer.h5"
 #     print("rHOG inferece has started. The oma database address is in ", oma_database_address)
 #     (oma_db, list_oma_species) = _utils_rhog.parse_oma_db(oma_database_address)

diff --git a/archive/analysis/main_bird.py b/archive/analysis/main_bird.py
@@ -2,8 +2,8 @@
 from dask.distributed import Client
 from dask_jobqueue import SLURMCluster
 
-from fastoma import _utils_subhog, _infer_subhog, _utils_roothog
-from fastoma._utils_subhog import logger_hog
+from FastOMA import _utils_subhog, _infer_subhog, _utils_roothog
+from FastOMA._utils_subhog import logger_hog
 
 if __name__ == '__main__':
 
@@ -26,7 +26,7 @@
         rHOG=rootHOG.  A subHOG itself is orthoxml_to_newick.py HOG.
         """
 
-        oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/fastoma/archive/OmaServer.h5"
+        oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/FastOMA/archive/OmaServer.h5"
         # in_folder+"omamer_database/oma_path/OmaServer.h5"
         print("rHOG inferece has started. The oma database address is in ", oma_database_address)
         (oma_db, list_oma_species) = _utils_rhog.parse_oma_db(oma_database_address)

diff --git a/archive/analysis/test_curnagle.py b/archive/analysis/test_curnagle.py
@@ -144,7 +144,7 @@ def infer_hogs_for_rhog_levels_recursively(sub_species_tree):
 # # import _inferhog
 # #
 # # # from _utils import logger_hog
-# # import fastoma._utils_rhog as _utils_rhog
+# # import FastOMA._utils_rhog as _utils_rhog
 # #
 # # # from distributed import get_client
 # # # from dask.distributed import rejoin, secede
@@ -158,7 +158,7 @@ def infer_hogs_for_rhog_levels_recursively(sub_species_tree):
 # #     file_folders = (address_rhogs_folder, gene_trees_folder, pickle_folder, species_tree_address)
 # #
 # #
-# #     oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/fastoma/archive/OmaServer.h5"
+# #     oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/FastOMA/archive/OmaServer.h5"
 # #     # in_folder+"omamer_database/oma_path/OmaServer.h5"
 # #     print("rHOG inferece has started. The oma database address is in ", oma_database_address)
 # #     (oma_db, list_oma_species) = _utils_rhog.parse_oma_db(oma_database_address)

diff --git a/archive/gethog3_from_rhog.py b/archive/gethog3_from_rhog.py
@@ -5,7 +5,7 @@
 import os
 
 
-# use this python code to convert gethog2 rhogs to fastoma
+# use this python code to convert gethog2 rhogs to FastOMA
 # check the following folder address
 # put the followings in  in in_folder
 # 1- gene_id_dic_xml.pickle
@@ -14,7 +14,7 @@
 
 
 # then run nextfolow pypilei
-# nextflow /work/FAC/FBM/DBC/cdessim2/default/smajidi1/pycharm_projects/fastoma/archive/gethog3_rhog.nf --input_folder in_folder   --output_folder out_folder -c  /work/FAC/FBM/DBC/cdessim2/default/smajidi1/pycharm_projects/fastoma/nextflow_slurm.config
+# nextflow /work/FAC/FBM/DBC/cdessim2/default/smajidi1/pycharm_projects/FastOMA/archive/gethog3_rhog.nf --input_folder in_folder   --output_folder out_folder -c  /work/FAC/FBM/DBC/cdessim2/default/smajidi1/pycharm_projects/FastOMA/nextflow_slurm.config
 
 
 

diff --git a/archive/test_curn.py b/archive/test_curn.py
@@ -347,7 +347,7 @@
 # # #     file_folders = (address_rhogs_folder, gene_trees_folder, pickle_folder, species_tree_address)
 # # #
 # # #
-# # #     oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/fastoma/archive/OmaServer.h5"
+# # #     oma_database_address = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/FastOMA/archive/OmaServer.h5"
 # # #     # in_folder+"omamer_database/oma_path/OmaServer.h5"
 # # #     print("rHOG inferece has started. The oma database address is in ", oma_database_address)
 # # #     (oma_db, list_oma_species) = _utils_rhog.parse_oma_db(oma_database_address)

diff --git a/archive/test_infer_subhogs.py b/archive/test_infer_subhogs.py
@@ -1,6 +1,6 @@
 
 
-from fastoma.infer_subhogs import infer_subhogs
+from FastOMA.infer_subhogs import infer_subhogs
 
 
 # --input-rhog-folder ./bb/ --parrallel True  --species-tree species_tree.nwk

diff --git a/fastoma/__init__.py b/fastoma/__init__.py
diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-name = 'fastoma'
+name = 'FastOMA'
 __version__ = None
 with open('{:s}/__init__.py'.format(name), 'rt') as fp:
     for line in fp:
@@ -27,10 +27,10 @@
     license='MIT',
     entry_points={
         'console_scripts': [
-            "infer-roothogs=fastoma.infer_roothogs:infer_roothogs",
-            "batch-roothogs=fastoma.batch_roothogs:batch_roothogs",
-            "infer-subhogs=fastoma.infer_subhogs:infer_subhogs",
-            "collect-subhogs=fastoma.collect_subhogs:collect_subhogs",
+            "infer-roothogs=FastOMA.infer_roothogs:infer_roothogs",
+            "batch-roothogs=FastOMA.batch_roothogs:batch_roothogs",
+            "infer-subhogs=FastOMA.infer_subhogs:infer_subhogs",
+            "collect-subhogs=FastOMA.collect_subhogs:collect_subhogs",
         ]
     },
 )
diff --git a/utils/orthoxml2family.py b/utils/orthoxml2family.py
@@ -4,7 +4,7 @@
 #
 from Bio import SeqIO
 
-from fastoma.zoo.hog.convert import extract_flat_groups_at_level
+from FastOMA.zoo.hog.convert import extract_flat_groups_at_level
 
 
 

diff --git a/utils/orthoxml2newick.py b/utils/orthoxml2newick.py
@@ -2,7 +2,7 @@
 
 
 
-from fastoma.zoo.hog.convert import orthoxml_to_newick
+from FastOMA.zoo.hog.convert import orthoxml_to_newick
 
 input_orthoxml = "folder/my_hogs.orthoxml"
 output_folder = "output_folder"
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@

		__packagename__ = "FastOMA"
		__version__ = "0.0.5"
Original file line number	Diff line number	Diff line change
Expand Up		@@ -11,6 +11,7 @@
		# import _config



		# from ._utils import logger_hog
		# import ._utils_rhog

Expand Down
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,7 +4,7 @@ @@
     #
     from Bio import SeqIO
-    from fastoma.zoo.hog.convert import extract_flat_groups_at_level
+    from FastOMA.zoo.hog.convert import extract_flat_groups_at_level
@@ Expand Down @@