PyPI - FunVIP - Versions diffs - 0.3.20__tar.gz → 0.3.22__tar.gz - Mend

FunVIP 0.3.20tar.gz → 0.3.22tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (222) hide show

{funvip-0.3.20 → funvip-0.3.22/FunVIP.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FunVIP
-Version: 0.3.20
+Version: 0.3.22
 Summary: Fungal Validation & Identification Pipeline
 Author-email: Changwan Seo <wan101010@snu.ac.kr>
 License: GPL-3.0
@@ -11,7 +11,7 @@ Requires-Dist: biopython==1.78
 Requires-Dist: ete3==3.1.3
 Requires-Dist: Cython
 Requires-Dist: dendropy
-Requires-Dist: GenMine>=1.0.13
+Requires-Dist: GenMine<1.2.0,>=1.1.0
 Requires-Dist: lxml
 Requires-Dist: matplotlib
 Requires-Dist: numpy

funvip-0.3.22/FunVIP.egg-info/SOURCES.txt ADDED Viewed

@@ -0,0 +1,217 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+FunVIP.egg-info/PKG-INFO
+FunVIP.egg-info/SOURCES.txt
+FunVIP.egg-info/dependency_links.txt
+FunVIP.egg-info/entry_points.txt
+FunVIP.egg-info/requires.txt
+FunVIP.egg-info/top_level.txt
+funvip/FunVIP_GUI.py
+funvip/__init__.py
+funvip/main.py
+funvip/data/Option_manager.xlsx
+funvip/data/__init__.py
+funvip/data/genus_line.txt
+funvip/external/MAFFT_LICENSE
+funvip/external/MAFFT_Windows.zip
+funvip/external/__init__.py
+funvip/external/BLAST_Windows/Uninstall-ncbi-blast-2.12.0+.exe
+funvip/external/BLAST_Windows/bin/blastn.exe
+funvip/external/BLAST_Windows/bin/cleanup-blastdb-volumes.py
+funvip/external/BLAST_Windows/bin/get_species_taxids.sh
+funvip/external/BLAST_Windows/bin/legacy_blast.pl
+funvip/external/BLAST_Windows/bin/makeblastdb.exe
+funvip/external/BLAST_Windows/bin/nghttp2.dll
+funvip/external/BLAST_Windows/bin/update_blastdb.pl
+funvip/external/BLAST_Windows/doc/README.txt
+funvip/external/FastTree_Windows/FastTree.exe
+funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/Gblocks.exe
+funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/nad3.pir
+funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/paths
+funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/Documentation/Gblocks_documentation.html
+funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/cox2.pir
+funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/cytb.pir
+funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/nad3.pir
+funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/nad5.pir
+funvip/external/RAxML_Windows/GPL-3.0.txt
+funvip/external/RAxML_Windows/README
+funvip/external/RAxML_Windows/raxmlHPC-PTHREADS-AVX2.exe
+funvip/external/iqtree/example.cf
+funvip/external/iqtree/example.nex
+funvip/external/iqtree/example.phy
+funvip/external/iqtree/models.nex
+funvip/external/iqtree/bin/iqtree2-click.exe
+funvip/external/iqtree/bin/iqtree2.exe
+funvip/external/iqtree/bin/libiomp5md.dll
+funvip/external/mmseqs_Windows/LICENSE.md
+funvip/external/mmseqs_Windows/README.md
+funvip/external/mmseqs_Windows/mmseqs.bat
+funvip/external/mmseqs_Windows/bin/busybox.exe
+funvip/external/mmseqs_Windows/bin/cygbz2-1.dll
+funvip/external/mmseqs_Windows/bin/cyggcc_s-seh-1.dll
+funvip/external/mmseqs_Windows/bin/cyggomp-1.dll
+funvip/external/mmseqs_Windows/bin/cygstdc++-6.dll
+funvip/external/mmseqs_Windows/bin/cygwin1.dll
+funvip/external/mmseqs_Windows/bin/cygz.dll
+funvip/external/mmseqs_Windows/bin/mmseqs.exe
+funvip/external/mmseqs_Windows/examples/QUERY.fasta
+funvip/external/mmseqs_Windows/matrices/PAM10.out
+funvip/external/mmseqs_Windows/matrices/PAM100.out
+funvip/external/mmseqs_Windows/matrices/PAM110.out
+funvip/external/mmseqs_Windows/matrices/PAM120.out
+funvip/external/mmseqs_Windows/matrices/PAM130.out
+funvip/external/mmseqs_Windows/matrices/PAM140.out
+funvip/external/mmseqs_Windows/matrices/PAM150.out
+funvip/external/mmseqs_Windows/matrices/PAM160.out
+funvip/external/mmseqs_Windows/matrices/PAM170.out
+funvip/external/mmseqs_Windows/matrices/PAM180.out
+funvip/external/mmseqs_Windows/matrices/PAM190.out
+funvip/external/mmseqs_Windows/matrices/PAM20.out
+funvip/external/mmseqs_Windows/matrices/PAM30.out
+funvip/external/mmseqs_Windows/matrices/PAM40.out
+funvip/external/mmseqs_Windows/matrices/PAM50.out
+funvip/external/mmseqs_Windows/matrices/PAM60.out
+funvip/external/mmseqs_Windows/matrices/PAM70.out
+funvip/external/mmseqs_Windows/matrices/PAM80.out
+funvip/external/mmseqs_Windows/matrices/PAM90.out
+funvip/external/mmseqs_Windows/matrices/VTML10.out
+funvip/external/mmseqs_Windows/matrices/VTML120.out
+funvip/external/mmseqs_Windows/matrices/VTML160.out
+funvip/external/mmseqs_Windows/matrices/VTML20.out
+funvip/external/mmseqs_Windows/matrices/VTML40.out
+funvip/external/mmseqs_Windows/matrices/VTML80.out
+funvip/external/mmseqs_Windows/matrices/blosum100.out
+funvip/external/mmseqs_Windows/matrices/blosum30.out
+funvip/external/mmseqs_Windows/matrices/blosum35.out
+funvip/external/mmseqs_Windows/matrices/blosum40.out
+funvip/external/mmseqs_Windows/matrices/blosum45.out
+funvip/external/mmseqs_Windows/matrices/blosum50.out
+funvip/external/mmseqs_Windows/matrices/blosum55.out
+funvip/external/mmseqs_Windows/matrices/blosum60.out
+funvip/external/mmseqs_Windows/matrices/blosum62.out
+funvip/external/mmseqs_Windows/matrices/blosum65.out
+funvip/external/mmseqs_Windows/matrices/blosum70.out
+funvip/external/mmseqs_Windows/matrices/blosum75.out
+funvip/external/mmseqs_Windows/matrices/blosum80.out
+funvip/external/mmseqs_Windows/matrices/blosum85.out
+funvip/external/mmseqs_Windows/matrices/blosum90.out
+funvip/external/mmseqs_Windows/matrices/blosum95.out
+funvip/external/mmseqs_Windows/matrices/nucleotide.out
+funvip/external/mmseqs_Windows/util/bash-completion.sh
+funvip/external/trimal.v1.4/trimAl/AUTHORS
+funvip/external/trimal.v1.4/trimAl/CHANGELOG
+funvip/external/trimal.v1.4/trimAl/LICENSE
+funvip/external/trimal.v1.4/trimAl/README
+funvip/external/trimal.v1.4/trimAl/bin/libgcc_s_dw2-1.dll
+funvip/external/trimal.v1.4/trimAl/bin/libstdc++-6.dll
+funvip/external/trimal.v1.4/trimAl/bin/trimal.exe
+funvip/external/trimal.v1.4/trimAl/scripts/check_codon_alignments.py
+funvip/external/trimal.v1.4/trimAl/scripts/compare_trimmed_msas.sh
+funvip/external/trimal.v1.4/trimAl/scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py
+funvip/external/trimal.v1.4/trimAl/scripts/generate_trimmed_msas.sh
+funvip/external/trimal.v1.4/trimAl/scripts/get_sequence_representative_from_alignment.py
+funvip/external/trimal.v1.4/trimAl/scripts/get_sequences_gaps_ratio.py
+funvip/external/trimal.v1.4/trimAl/scripts/remove_shorter_sequences.py
+funvip/external/trimal.v1.4/trimAl/scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py
+funvip/external/trimal.v1.4/trimAl/scripts/set_manual_boundaries.py
+funvip/external/trimal.v1.4/trimAl/source/alignment.cpp
+funvip/external/trimal.v1.4/trimAl/source/alignment.h
+funvip/external/trimal.v1.4/trimAl/source/alignment.o
+funvip/external/trimal.v1.4/trimAl/source/autAlignment.cpp
+funvip/external/trimal.v1.4/trimAl/source/autAlignment.o
+funvip/external/trimal.v1.4/trimAl/source/compareFiles.cpp
+funvip/external/trimal.v1.4/trimAl/source/compareFiles.h
+funvip/external/trimal.v1.4/trimAl/source/compareFiles.o
+funvip/external/trimal.v1.4/trimAl/source/defines.h
+funvip/external/trimal.v1.4/trimAl/source/main.cpp
+funvip/external/trimal.v1.4/trimAl/source/makefile
+funvip/external/trimal.v1.4/trimAl/source/makefile.MacOS
+funvip/external/trimal.v1.4/trimAl/source/readAl.cpp
+funvip/external/trimal.v1.4/trimAl/source/readal.exe
+funvip/external/trimal.v1.4/trimAl/source/rwAlignment.cpp
+funvip/external/trimal.v1.4/trimAl/source/rwAlignment.o
+funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.cpp
+funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.h
+funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.o
+funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.cpp
+funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.h
+funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.o
+funvip/external/trimal.v1.4/trimAl/source/statAl.cpp
+funvip/external/trimal.v1.4/trimAl/source/statal.exe
+funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.cpp
+funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.h
+funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.o
+funvip/external/trimal.v1.4/trimAl/source/statisticsFiles.cpp
+funvip/external/trimal.v1.4/trimAl/source/statisticsFiles.h
+funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.cpp
+funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.h
+funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.o
+funvip/external/trimal.v1.4/trimAl/source/utils.cpp
+funvip/external/trimal.v1.4/trimAl/source/utils.h
+funvip/external/trimal.v1.4/trimAl/source/utils.o
+funvip/external/trimal.v1.4/trimAl/source/values.h
+funvip/preset/.gitignore
+funvip/preset/accurate.yaml
+funvip/preset/fast.yaml
+funvip/src/.gitignore
+funvip/src/__init__.py
+funvip/src/align.py
+funvip/src/cluster.py
+funvip/src/command.py
+funvip/src/concatenate.py
+funvip/src/dataset.py
+funvip/src/ext.py
+funvip/src/hasher.py
+funvip/src/initialize.py
+funvip/src/logger.py
+funvip/src/logics.py
+funvip/src/modeltest.py
+funvip/src/ncbi.py
+funvip/src/opt_generator.py
+funvip/src/reporter.py
+funvip/src/save.py
+funvip/src/search.py
+funvip/src/tool.py
+funvip/src/tree.py
+funvip/src/tree_interpretation.py
+funvip/src/tree_interpretation_pipe.py
+funvip/src/trim.py
+funvip/src/validate_input.py
+funvip/src/validate_option.py
+funvip/src/validation.py
+funvip/src/version.py
+funvip/src/__pycache__/CATV_pipe.cpython-310.pyc
+funvip/src/__pycache__/CAT_V.cpython-310.pyc
+funvip/src/__pycache__/CAT_V.cpython-39.pyc
+funvip/src/__pycache__/CAT_V_pipe.cpython-39.pyc
+funvip/src/__pycache__/__init__.cpython-310.pyc
+funvip/src/__pycache__/__init__.cpython-39.pyc
+funvip/src/__pycache__/align.cpython-310.pyc
+funvip/src/__pycache__/cluster.cpython-39.pyc
+funvip/src/__pycache__/dataset.cpython-39.pyc
+funvip/src/__pycache__/ext.cpython-310.pyc
+funvip/src/__pycache__/ext.cpython-39.pyc
+funvip/src/__pycache__/hasher.cpython-39.pyc
+funvip/src/__pycache__/initialize.cpython-39.pyc
+funvip/src/__pycache__/io.cpython-310.pyc
+funvip/src/__pycache__/io.cpython-39.pyc
+funvip/src/__pycache__/logger.cpython-39.pyc
+funvip/src/__pycache__/modeltest.cpython-39.pyc
+funvip/src/__pycache__/multigene.cpython-39.pyc
+funvip/src/__pycache__/ncbi.cpython-39.pyc
+funvip/src/__pycache__/opt_generator.cpython-39.pyc
+funvip/src/__pycache__/reporter.cpython-39.pyc
+funvip/src/__pycache__/search.cpython-39.pyc
+funvip/src/__pycache__/tool.cpython-39.pyc
+funvip/src/__pycache__/validation.cpython-39.pyc
+funvip/src/__pycache__/visualize.cpython-39.pyc
+funvip/src/templates/template.html
+funvip/test_dataset/penicillium/Options.config
+funvip/test_dataset/penicillium/preset.yaml
+funvip/test_dataset/penicillium/DB/DB_Penicillium.xlsx
+funvip/test_dataset/penicillium/Query/Query.xlsx
+funvip/test_dataset/terrei/preset.yaml
+funvip/test_dataset/terrei/DB/FunVIP_Aspergillus_db.xlsx
+funvip/test_dataset/terrei/Query/FunVIP_Aspergillus_query.xlsx

{funvip-0.3.20/funvip → funvip-0.3.22}/FunVIP.egg-info/requires.txt RENAMED Viewed

@@ -2,7 +2,7 @@ biopython==1.78
 ete3==3.1.3
 Cython
 dendropy
-GenMine>=1.0.13
+GenMine<1.2.0,>=1.1.0
 lxml
 matplotlib
 numpy

funvip-0.3.22/FunVIP.egg-info/top_level.txt ADDED Viewed

	@@ -0,0 +1 @@
1	+ funvip

funvip-0.3.22/MANIFEST.in ADDED Viewed

@@ -0,0 +1,5 @@
+recursive-include funvip/data *
+recursive-include funvip/external *
+recursive-include funvip/preset *
+recursive-include funvip/src *
+recursive-include funvip/test_dataset *

{funvip-0.3.20/funvip/FunVIP.egg-info → funvip-0.3.22}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FunVIP
-Version: 0.3.20
+Version: 0.3.22
 Summary: Fungal Validation & Identification Pipeline
 Author-email: Changwan Seo <wan101010@snu.ac.kr>
 License: GPL-3.0
@@ -11,7 +11,7 @@ Requires-Dist: biopython==1.78
 Requires-Dist: ete3==3.1.3
 Requires-Dist: Cython
 Requires-Dist: dendropy
-Requires-Dist: GenMine>=1.0.13
+Requires-Dist: GenMine<1.2.0,>=1.1.0
 Requires-Dist: lxml
 Requires-Dist: matplotlib
 Requires-Dist: numpy

{funvip-0.3.20 → funvip-0.3.22}/README.md RENAMED Viewed

@@ -1,10 +1,9 @@
 [![DOI](https://zenodo.org/badge/588465720.svg)](https://zenodo.org/doi/10.5281/zenodo.10714946)
-#### This is Beta release. Unstable. We're eagaring bug reports
+#### This is Beta release. Bug reports are welcomed
 ## Scheduling
 ### Beta release part 1 (2023 Feburary ~ As paper published, ver 0.3)
-- ~~Will operate normally most of the case~~ We tried our best, but it's still very buggy. Please report bugs for us
 - Will be tested by our lab memebers to fix bugs and advance features
 ### Beta release part 2 (As paper published ~ When pipeline gets stabled, ver 0.4)
@@ -13,77 +12,75 @@
 ### Stable release (ver 1.0)
 # FunVIP
 "Fun"gal "V"alidation & "I"dentification "P"ipeline
-A automatic tree-based sequence identification pipeline for fungal species
+An automatic tree-based sequence identification and validation pipeline for fungal species
 - Automatic tree-based identification
 - Works with multigene
 - Data validation algorithm implemented
-# See [tutorial](https://github.com/Changwanseo/FunID/blob/main/tutorial/tutorial.md) for detailed usage
+# See [tutorial](https://github.com/Changwanseo/FunVIP/blob/main/tutorial/tutorial.md) for detailed usage
 ## Requirements
-- Conda environment (See https://www.anaconda.com/products/individual to install)
+- Conda environment (See [https://www.anaconda.com/products/individual](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) to how to install conda environment)
 <!--
 ## Installation with conda (May not work with Linux or Mac)
-1. ```conda create -n FunID python=3.10```
-2. ```conda activate FunID```
-3. ```conda install -c cwseo FunID```
-4. run ```FunID --test Penicillium ``` to check installation
+1. ```conda create -n FunVO{ python=3.10```
+2. ```conda activate FunVIP```
+3. ```conda install -c cwseo FunVIP```
+4. run ```FunVIP --test Terrei --email [your email] ``` to check installation
 If this one fails, use next one
 -->
 ## Windows
-1. Install visual c++ [here](https://visualstudio.microsoft.com/ko/visual-cpp-build-tools/)
-2. ```conda create -n FunID python=3.9```
-3. ```conda activate FunID```
-4. ```pip install FunID```
-5. run ```FunID --test Penicillium ``` to check installation
+1. Install visual c++ [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/)
+2. ```conda create -n FunVIP python>=3.8```
+3. ```conda activate FunVIP```
+4. ```pip install FunVIP```
+5. run ```FunVIP --test Terrei --email [your email] ``` to check installation
 * For upgrade use this command
-``` pip install FunID --upgrade ```
+``` pip install FunVIP --upgrade ```
 ## Linux
-1. ```conda create -n FunID python=3.9```
-2. ```conda activate FunID```
-3. ```pip install FunID```
+1. ```conda create -n FunVIP python>=3.8```
+2. ```conda activate FunVIP```
+3. ```pip install FunVIP```
 4. ```conda install -c bioconda raxml iqtree modeltest-ng mmseqs2 "blast>=2.12" mafft trimal gblocks fasttree```
-5. run ```FunID --test Penicillium ``` to check installation
+5. run ```FunVIP --test Terrei --email [your email] ``` to check installation
 * For intel mac system, this method probably work, but we couldn't test it because we don't have any intel mac device. We're looking for feedbacks in intel mac
 ## Apple Silicon Mac
-1. ```CONDA_SUBDIR=osx-64 conda create -n FunID python=3.10```
-2. ```conda activate FunID```
+1. ```CONDA_SUBDIR=osx-64 conda create -n FunVIP python>=3.8```
+2. ```conda activate FunVIP```
 3. ```conda config --env --set subdir osx-64```
 4. ```conda install pyqt```
-5. ```pip install FunID```
+5. ```pip install FunVIP```
 6. ```conda install -c bioconda raxml iqtree mmseqs2 "blast>=2.12" mafft trimal gblocks fasttree```
-7. run ```FunID --test Penicillium ``` to check installation
+7. run ```FunVIP --test Terrei --email [your email] ``` to check installation
-## Installation from source (For developers)
+## Installation from source (For developers and core users)
 * this is for developmental steps
-1. ```git clone https://github.com/Changwanseo/FunID.git```
-2. Move to ```~/FunID```
-3. ```conda create -n FunID python=3.10```
-4. ```conda activate FunID```
+1. ```git clone https://github.com/Changwanseo/FunVIP.git```
+2. Move to ```~/FunVIP```
+3. ```conda create -n FunVIP python=3.10```
+4. ```conda activate FunVIP```
 5. ```pip install ./```
-6. run ```FunID --test Penicillium ``` to check installation
+6. run ```FunVIP --test Terrei --email [your email]``` to check installation
 ## Usage
-```FunID --db {Your database file} --query {Your query file} --email {Your email} --gene {Your genes} --preset {fast or accurate}```
+```FunVIP --db {Your database file} --query {Your query file} --email {Your email} --gene {Your genes} --preset {fast or accurate}```
 ### Example
-```FunID --db Penicillium.xlsx --query Query.xlsx --email {Your email} --gene ITS BenA RPB2 CaM --preset fast```
+```FunVIP --db Penicillium.xlsx --query Query.xlsx --email {Your email} --gene ITS BenA RPB2 CaM --preset fast```
 \* See documentation for detailed usage
@@ -101,12 +98,12 @@ If this one fails, use next one
 ## How to make database?
-  ![Fig 2 FunID interface, usage, and input example](https://github.com/Changwanseo/FunID/assets/64393882/78e5dd58-a656-4395-bda9-0ee671411e2c)
+![Fig 2 Database and command configuration of FunID (ver2) ](https://github.com/Changwanseo/FunVIP/assets/64393882/9ba71eb9-91e9-4c0b-ac60-b9b7be993694)
-[See example database here](https://github.com/Changwanseo/FunID/blob/main/funid/test_dataset/penicillium/DB/DB_Penicillium.xlsx)
+[See example database here](https://github.com/Changwanseo/FunVIP/blob/main/funvip/test_dataset/penicillium/DB/DB_Penicillium.xlsx)
 <!--##
@@ -132,7 +129,7 @@ tabular (```.xlsx```, ```.csv```,  ```.parquet```, ```.ftr```) form
 * ```/Tree/{section}_{gene}.svg``` : Final collapsed tree in svg format. Can be edited in vector graphics programs, or in powerpoint (by ungroup)
 * ```/Tree/{section}_{gene}_original.svg ``` : Uncollapsed tree for inspection
-## How does FunID work?
+## How does FunVIP work?
 ![figure1 - ver4](https://github.com/Changwanseo/FunID/assets/64393882/6a366d32-6aaf-4d0c-8102-8c7dd5fda4c2)

FunVIP 0.3.20__tar.gz → 0.3.22__tar.gz

FunVIP 0.3.20tar.gz → 0.3.22tar.gz