apscale-gui 3.3.0__tar.gz → 3.3.2__tar.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 (17) hide show
  1. {apscale_gui-3.3.0/apscale_gui.egg-info → apscale_gui-3.3.2}/PKG-INFO +9 -4
  2. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/README.md +6 -2
  3. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui/apscale_gui.py +6 -5
  4. {apscale_gui-3.3.0 → apscale_gui-3.3.2/apscale_gui.egg-info}/PKG-INFO +9 -4
  5. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui.egg-info/requires.txt +2 -1
  6. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/setup.py +4 -3
  7. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/LICENSE +0 -0
  8. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/MANIFEST.in +0 -0
  9. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui/__init__.py +0 -0
  10. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui/__main__.py +0 -0
  11. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui/_user_data/.DS_Store +0 -0
  12. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui/_user_data/user_data.txt +0 -0
  13. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui.egg-info/SOURCES.txt +0 -0
  14. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui.egg-info/dependency_links.txt +0 -0
  15. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui.egg-info/entry_points.txt +0 -0
  16. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui.egg-info/top_level.txt +0 -0
  17. {apscale_gui-3.3.0 → apscale_gui-3.3.2}/setup.cfg +0 -0
{apscale_gui-3.3.0/apscale_gui.egg-info → apscale_gui-3.3.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.4
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  Name: apscale_gui
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- Version: 3.3.0
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+ Version: 3.3.2
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  Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
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  Home-page: https://github.com/TillMacher/apscale_gui
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  Author: Till-Hendrik Macher
@@ -14,7 +14,7 @@ Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: apscale>=4.1.4
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  Requires-Dist: apscale_blast>=1.2.7
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- Requires-Dist: boldigger3>=2.1.4
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+ Requires-Dist: boldigger3>=3.0.3
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  Requires-Dist: demultiplexer2>=1.1.6
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  Requires-Dist: ete3>=3.1.3
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  Requires-Dist: lxml_html_clean>=0.4.2
@@ -32,6 +32,7 @@ Requires-Dist: requests>=2.32.3
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  Requires-Dist: beautifulsoup4>=4.13.4
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  Requires-Dist: lxml>=6.0.0
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  Requires-Dist: asyncio>=4.0.0
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+ Requires-Dist: stqdm>=0.0.5
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  Dynamic: author
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  Dynamic: author-email
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  Dynamic: classifier
@@ -84,7 +85,10 @@ To update APSCALE GUI to the latest version, use:
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  `pip install --upgrade apscale_gui`
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- Note: APSCALE and APSCALE GUI requires python3.12 or higher!
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+ ### Important notes:
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+ * APSCALE and APSCALE GUI requires python3.12 or higher!
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+ * If possible, use the apscale4 environment.
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+ * Apscale projects created with apscale v3 or older are not compatible with apscale v4. Please create a new project.
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  ---
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@@ -181,7 +185,7 @@ Settings_My_new_project.xlsx
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  18. The sequencing results can now be taxonomically assigned using [APSCALE-blast](https://github.com/TillMacher/apscale_blast).
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- 19. APSCALE-blast is based on blast+ and performs the taxonomic assignments against [pre-compiled local databases](https://seafile.rlp.net/d/474b9682a5cb4193a6ad/). These can be indivudally downloaded or batch-downloaded and extracted using the "Download All Latest Databases" button. The APSCALE databases are stored in the folder "APSCALE_projects/APSCALE_databases".
188
+ 19. APSCALE-blast is based on blast+ and performs the taxonomic assignments against [pre-compiled local databases](https://seafile.rlp.net/d/c172d076de1e4c45b594/). These can be indivudally downloaded or batch-downloaded and extracted using the "Download All Latest Databases" button. The APSCALE databases are stored in the folder "APSCALE_projects/APSCALE_databases".
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  20. To perform the taxonomic assignment, simply select the .fasta file and the database to begin the blast search.
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@@ -209,4 +213,5 @@ When using APSCALE, please cite the following:
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  * [VSEARCH](https://peerj.com/articles/2584/)
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  * [Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200)
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  * [BOLDigger](https://mbmg.pensoft.net/article/53535/)
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+ * [BLAST+](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-421)
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  * [The specific database for local BLASTn search](https://github.com/TillMacher/apscale_blast?tab=readme-ov-file#available-databases).
{apscale_gui-3.3.0 → apscale_gui-3.3.2}/README.md RENAMED
@@ -38,7 +38,10 @@ To update APSCALE GUI to the latest version, use:
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  `pip install --upgrade apscale_gui`
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- Note: APSCALE and APSCALE GUI requires python3.12 or higher!
41
+ ### Important notes:
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+ * APSCALE and APSCALE GUI requires python3.12 or higher!
43
+ * If possible, use the apscale4 environment.
44
+ * Apscale projects created with apscale v3 or older are not compatible with apscale v4. Please create a new project.
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  ---
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@@ -135,7 +138,7 @@ Settings_My_new_project.xlsx
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  18. The sequencing results can now be taxonomically assigned using [APSCALE-blast](https://github.com/TillMacher/apscale_blast).
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138
- 19. APSCALE-blast is based on blast+ and performs the taxonomic assignments against [pre-compiled local databases](https://seafile.rlp.net/d/474b9682a5cb4193a6ad/). These can be indivudally downloaded or batch-downloaded and extracted using the "Download All Latest Databases" button. The APSCALE databases are stored in the folder "APSCALE_projects/APSCALE_databases".
141
+ 19. APSCALE-blast is based on blast+ and performs the taxonomic assignments against [pre-compiled local databases](https://seafile.rlp.net/d/c172d076de1e4c45b594/). These can be indivudally downloaded or batch-downloaded and extracted using the "Download All Latest Databases" button. The APSCALE databases are stored in the folder "APSCALE_projects/APSCALE_databases".
139
142
 
140
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  20. To perform the taxonomic assignment, simply select the .fasta file and the database to begin the blast search.
141
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@@ -163,4 +166,5 @@ When using APSCALE, please cite the following:
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  * [VSEARCH](https://peerj.com/articles/2584/)
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  * [Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200)
165
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  * [BOLDigger](https://mbmg.pensoft.net/article/53535/)
169
+ * [BLAST+](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-421)
166
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  * [The specific database for local BLASTn search](https://github.com/TillMacher/apscale_blast?tab=readme-ov-file#available-databases).
{apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui/apscale_gui.py RENAMED
@@ -59,6 +59,7 @@ from boldigger3 import select_top_hit
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  from boldigger3 import download_database
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  import requests
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+
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  # help texts
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  n_cores_help = """
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  All settings required by Apscale are configured within the project’s settings file. Each processing step has its
@@ -833,9 +834,9 @@ def main():
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  st.info(f'{n_databases} databases available')
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  if st.button('Open Database Hub', use_container_width=True):
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- webbrowser.open('https://seafile.rlp.net/d/474b9682a5cb4193a6ad/')
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+ webbrowser.open('https://seafile.rlp.net/d/c172d076de1e4c45b594/')
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  if st.button('Download All Latest Databases', use_container_width=True):
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- public_url = 'https://seafile.rlp.net/d/474b9682a5cb4193a6ad/?p=%2FLatest&mode=list'
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+ public_url = 'https://seafile.rlp.net/d/c172d076de1e4c45b594/?p=%2FLatest&mode=list'
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  download_seafile_zip(public_url, database_folder)
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  if st.button('Open APSCALE database folder', use_container_width=True):
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  open_folder(database_folder)
@@ -1121,11 +1122,11 @@ def main():
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  with st.expander("⚖️ Thresholds", expanded=False):
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  col1, col2 = st.columns(2)
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  with col1:
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- st.text_input(label='Species (%)', key='t_species', value=97)
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- st.text_input(label='Family (%)', key='t_family', value=90)
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- st.text_input(label='Class (%)', key='t_class', value=85)
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+ st.text_input(label='Species (%)', key='t_species', value=98)
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  st.text_input(label='Genus (%)', key='t_genus', value=95)
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+ st.text_input(label='Family (%)', key='t_family', value=90)
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  st.text_input(label='Order (%)', key='t_order', value=87)
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+ st.text_input(label='Class (%)', key='t_class', value=85)
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  with col2:
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  st.selectbox(label='Masking', key='masking', options=[True, False], index=0)
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  filter_mode_dict = {'similarity -> e-value -> rating (optional)':"1", 'e-value -> similarity -> rating (optional)':"2", 'similarity -> rating (optional)':"3"}
{apscale_gui-3.3.0 → apscale_gui-3.3.2/apscale_gui.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: apscale_gui
3
- Version: 3.3.0
3
+ Version: 3.3.2
4
4
  Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
5
5
  Home-page: https://github.com/TillMacher/apscale_gui
6
6
  Author: Till-Hendrik Macher
@@ -14,7 +14,7 @@ Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: apscale>=4.1.4
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  Requires-Dist: apscale_blast>=1.2.7
17
- Requires-Dist: boldigger3>=2.1.4
17
+ Requires-Dist: boldigger3>=3.0.3
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  Requires-Dist: demultiplexer2>=1.1.6
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  Requires-Dist: ete3>=3.1.3
20
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  Requires-Dist: lxml_html_clean>=0.4.2
@@ -32,6 +32,7 @@ Requires-Dist: requests>=2.32.3
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  Requires-Dist: beautifulsoup4>=4.13.4
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  Requires-Dist: lxml>=6.0.0
34
34
  Requires-Dist: asyncio>=4.0.0
35
+ Requires-Dist: stqdm>=0.0.5
35
36
  Dynamic: author
36
37
  Dynamic: author-email
37
38
  Dynamic: classifier
@@ -84,7 +85,10 @@ To update APSCALE GUI to the latest version, use:
84
85
 
85
86
  `pip install --upgrade apscale_gui`
86
87
 
87
- Note: APSCALE and APSCALE GUI requires python3.12 or higher!
88
+ ### Important notes:
89
+ * APSCALE and APSCALE GUI requires python3.12 or higher!
90
+ * If possible, use the apscale4 environment.
91
+ * Apscale projects created with apscale v3 or older are not compatible with apscale v4. Please create a new project.
88
92
 
89
93
  ---
90
94
 
@@ -181,7 +185,7 @@ Settings_My_new_project.xlsx
181
185
 
182
186
  18. The sequencing results can now be taxonomically assigned using [APSCALE-blast](https://github.com/TillMacher/apscale_blast).
183
187
 
184
- 19. APSCALE-blast is based on blast+ and performs the taxonomic assignments against [pre-compiled local databases](https://seafile.rlp.net/d/474b9682a5cb4193a6ad/). These can be indivudally downloaded or batch-downloaded and extracted using the "Download All Latest Databases" button. The APSCALE databases are stored in the folder "APSCALE_projects/APSCALE_databases".
188
+ 19. APSCALE-blast is based on blast+ and performs the taxonomic assignments against [pre-compiled local databases](https://seafile.rlp.net/d/c172d076de1e4c45b594/). These can be indivudally downloaded or batch-downloaded and extracted using the "Download All Latest Databases" button. The APSCALE databases are stored in the folder "APSCALE_projects/APSCALE_databases".
185
189
 
186
190
  20. To perform the taxonomic assignment, simply select the .fasta file and the database to begin the blast search.
187
191
 
@@ -209,4 +213,5 @@ When using APSCALE, please cite the following:
209
213
  * [VSEARCH](https://peerj.com/articles/2584/)
210
214
  * [Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200)
211
215
  * [BOLDigger](https://mbmg.pensoft.net/article/53535/)
216
+ * [BLAST+](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-421)
212
217
  * [The specific database for local BLASTn search](https://github.com/TillMacher/apscale_blast?tab=readme-ov-file#available-databases).
{apscale_gui-3.3.0 → apscale_gui-3.3.2}/apscale_gui.egg-info/requires.txt RENAMED
@@ -1,6 +1,6 @@
1
1
  apscale>=4.1.4
2
2
  apscale_blast>=1.2.7
3
- boldigger3>=2.1.4
3
+ boldigger3>=3.0.3
4
4
  demultiplexer2>=1.1.6
5
5
  ete3>=3.1.3
6
6
  lxml_html_clean>=0.4.2
@@ -18,3 +18,4 @@ requests>=2.32.3
18
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  beautifulsoup4>=4.13.4
19
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  lxml>=6.0.0
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20
  asyncio>=4.0.0
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+ stqdm>=0.0.5
{apscale_gui-3.3.0 → apscale_gui-3.3.2}/setup.py RENAMED
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
5
5
 
6
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  setuptools.setup(
7
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  name="apscale_gui",
8
- version="3.3.0",
8
+ version="3.3.2",
9
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  author="Till-Hendrik Macher",
10
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  author_email="macher@uni-trier.de",
11
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  description="Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface",
@@ -17,7 +17,7 @@ setuptools.setup(
17
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  install_requires = [
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  "apscale>=4.1.4",
19
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  "apscale_blast>=1.2.7",
20
- "boldigger3>=2.1.4",
20
+ "boldigger3>=3.0.3",
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  "demultiplexer2>=1.1.6",
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  "ete3>=3.1.3",
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  "lxml_html_clean>=0.4.2",
@@ -34,7 +34,8 @@ setuptools.setup(
34
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  "requests>=2.32.3",
35
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  "beautifulsoup4>=4.13.4",
36
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  "lxml>=6.0.0",
37
- "asyncio>=4.0.0"
37
+ "asyncio>=4.0.0",
38
+ "stqdm>=0.0.5"
38
39
  ],
39
40
  include_package_data = True,
40
41
  classifiers=[
{apscale_gui-3.3.0 → apscale_gui-3.3.2}/LICENSE RENAMED
File without changes
{apscale_gui-3.3.0 → apscale_gui-3.3.2}/MANIFEST.in RENAMED
File without changes
{apscale_gui-3.3.0 → apscale_gui-3.3.2}/setup.cfg RENAMED
File without changes