New python and biopython versions

.github/workflows/ci.yml

@@ -5,7 +5,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: ["3.9", "3.10"]
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python-version }}
@@ -26,13 +26,13 @@ jobs:
   test-full:
     runs-on: macos-latest
     env:
-      PYTHON: '3.9'
+      PYTHON: "3.10"
     steps:
     - uses: actions/checkout@master
     - name: Setup Python
       uses: actions/setup-python@master
       with:
-        python-version: 3.9
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         pip install -r requirements.txt
@@ -87,4 +87,4 @@ jobs:
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           BRANCH: gh-pages
-          FOLDER: docs/_build/html
+          FOLDER: docs/_build/html

orthosnap/version.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.1.0"

requirements.txt

@@ -1,3 +1,14 @@
-biopython==1.78
-numpy==1.20.1
-tqdm==4.58.0
+biopython==1.81
+coverage==7.3.2
+Cython==3.0.4
+exceptiongroup==1.1.3
+iniconfig==2.0.0
+mock==5.1.0
+numpy==1.24.0
+packaging==23.2
+pluggy==1.3.0
+pytest==7.4.2
+pytest-cov==4.1.0
+pytest-mock==3.0.0
+tomli==2.0.1
+tqdm==4.66.1

setup.py

@@ -12,13 +12,12 @@
     "Operating System :: OS Independent",
     "Intended Audience :: Science/Research",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
     "Topic :: Scientific/Engineering",
 ]
 
-REQUIRES = ["biopython==1.78", "numpy==1.20.1", "tqdm==4.58.0"]
+REQUIRES = ["biopython>=1.81", "numpy>=1.24.0", "tqdm>=4.66.1"]
 
 setup(
     name="orthosnap",
@@ -36,7 +35,7 @@
     install_requires=REQUIRES,
 )
 
-## push new version to pypi
+# push new version to pypi
 # rm -rf dist
 # python3 setup.py sdist bdist_wheel --universal
 # twine upload dist/* -r pypi

tests/samples/OG0000010.renamed.fa.mafft.clipkit.orthosnap.4.fa

@@ -1,100 +1,100 @@
->Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_09150-RA
-MGSMHEAG----------------------------------------------------
+>Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate
+M-----------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
-----------------------SRPAADAD---MDTDR------VHPEAV----------
------SNSERDFEKQDSKPEYRDAFGDEEYAEVKYKTLSWWQCGFLMVAETVSLGILSLP
-AVV---AALGLVPAIILLVALGLMSTYTGYTIGQFKWAYPHIHSMGDAGEVIMGRFGREL
-FGTGQLLLVVFIMASHILTFTVAMNSITDHGTCSIVFGVVGLVISFVLCLPRTLAKVSFL
-SVASFISVFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAFLAVCNIVFSFCRLFLHFIS
-FMDRTDRTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCLYIVAAVVIYCYAGDDVTSP
-ALGSASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWR-HSDRMHKRDLVATGSWV
-LIGLATWIVAWIIAEAIPVFNNLLSLVASLFASWFTYGFSALFWLYLNKGRFFSTPMKTA
-LTILNVVIMGIACCICGLGLYVSGKALHDDPSSASF------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------------------SCANNA---------------------------
+FGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM
+SMASCISIVTATVVTMIAIGVQAPDHVHVDATTEVSFQDAFLAVTNIIFAY---------
+--------IAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASP
+ALSSAGPLMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFR-GSAHMHQNSFLAIGSWV
+AIALGVWVVAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKIC
+LTIVNFLILAFACALCGMGLYVSGKSIHDSSSKASW------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
->Aspergillus_fumigatus_Af293|EAL84262.1
-MGSMHEAG----------------------------------------------------
+---------------------------TCKNNAT--------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
-----------------------SRPAAGAD---MDTDR------VHPEAV----------
------SDNERDFEKQDSKPEYQDAFGDEEYAEVKYKTLSWC-------------------
+----------------------------------------------------------TT
+>Aspergillus_fumigatus_Af293|EAL85095.2-duplicate
+M---------------------MLWLK---------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
--------VFSAVLIVMIAVGVQRPWHGGLNATVDTNLYKAFLAVCNIVFSFCRLFLHFSS
-FMDRTNKTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCLYIIAAVVIYCYAGDDVTSP
-ALGSASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWR-HSDRMHKRDLVATGSWV
-LIGLATWIVAWIIAEAIPVFNNLLSLVREVLVV-----ICTMIW-----ERVLIAPSVTA
-FRLF------------PLALFVATR----DPRSIG-------------------------
+--------------------RRNMLMGRRQMTRLEM------------------------
+-------------------------KNAERSNIV-------SCRGVMVAENISLGILSLS
+SAV---ATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQIHSMGDAGELLMGRFGREL
+FGIGQLLFLIFLMASHILTFSVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM
+SMASCISIVTATVVTMIAIGVQAPDHVHVNVTTKVSFQDAFLAVTNIIFAY---------
+--------IAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASP
+ALSSAGPLMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFR-GSAHMHQNSFLAIGSWV
+AIALGVWVVAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKIC
+LTIVNFFILAFACALCGMGLYVSGKSIHDSSSKASW------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+---------------------------TCKNNAT--------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
+----------------------------------------------------------TT
+>Aspergillus_fischeri_NRRL181|XP_001261692.1
+M-----------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
->Aspergillus_fischeri_NRRL181|XP_001267441.1
-MGSMLEAG----------------------------------------------------
+-------------------------AVSRD---LEA----------PAVVNDP-------
+---TAYDATVEKKEYADGTPANDPFGNEECGEVKYRVMSWWQCGTLMVAENISLGILSLP
+SAV---ATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQVHSMGDAGELLMGRFGREL
+FGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM
+SMASCISIVTATVVTMIAIGVQAPEHVHVDATTEVSFQDAFLAVTNIIFAY---------
+--------IAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASP
+ALSSAGPVMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFR-GSAHMHQNSFLAIGSWV
+AIALSVWVVAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKIC
+LTIVNFLILAFACALCGMGLYVSGKSIHDSSSKASW------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
-----------------------SRPAADAE---MDTDR------VHPEAV----------
------SDGERDFEKQDSKPEYQDAFGDEEYAEVKYKTLSWCH------GCRDSVTGYSLP
-ASG---GGLGPCP---------------------FKWAYPHIHSMGDAGEVIMGRFGREL
-FGTGQLLLVVFIMASHILTFTVAMNSITDHGTCSIVFGVVGLVISFVLCLPRTLAKVSFL
-SVASFISVFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAFLAVCNIVFSF---------
---------SGHVAFFGFMAELKNPRDYPKSLFLLQGIDTCLYIVAAVVIYCYAGDDVTSP
-ALGSASIVVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWR-HSDRMHKRDLVATGSWV
-LIGLATWIVAWIIAEAIPVFNNLLSLVASLFASWFTYGFSALFWLYLNKGRFFSTPMKTA
-LTILNVVIMGIACCICGLGLYVSGKALHDDPSSASF------------------------
 ------------------------------------------------------------
+---------------------------TCKNNAT--------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------------------SCANNA---------------------------
 ------------------------------------------------------------
+>Aspergillus_niger_CBS_513.88|XP_001401336.1
+M-----------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
->Aspergillus_niger_CBS_513.88|XP_001400898.1
-M--AHPTG----------------------------------------------------
+------------------------APTTRD---LEA----------LTVHHDS-------
+-DIMADDLAEKKVSANESPPENDPFGNEECGEVKYRVMKWWHCGILMIAENISLGILSLP
+SAV---ATLGIVPSIFLILGLSGISWYTGYVIGQFKLRYPQVHSMGDAGEILFGRIGREI
+LFFGQLLFCIFLMSSHILTFTVLFNTITGHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM
+SLASCTSITVATIVTMVAIAMQAPDHVQVDITTHPSFSTAFLSVTNIVFAF---------
+--------IAHVAFFGFASEMEDPRDFPKSLAMLQVTDTTMYIVTAMVIYRYAGPDVASP
+ALSSAGPLMSKVAYGLAIPTVIIAGVVFGHVASKYIYVRVWR-GSPQMHTNSLAAVGSWV
+AIALGVWVIAWIIAESIPVFNDLLSLISSLFGSWFSYGLPAMFWLVMNRGQYTASPRKIF
+LTIVNLVIFGIACAICGLGLYVSGKAIHDSSSSASW------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
-----------------------DKVDSHLN---VQTGQFFQDGREEPYLH----------
-------DAEEKQDEKKGSPIYNDTFGDEEYAEVKYKVLSWWQCGFLMVAETVSLGILSLP
-AVV---ATLGLAPAIVLIVGLGLLATYTGYVIGQFRWRYPHVQNLADAGEILFGSIGREI
-FGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFGVVGLVICFLLGLPRTSANVSYL
-SVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLYEAFLAVCNIVFSF---------
---------SGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGPNVTSP
-ALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFR-HGDRMHSRDLLATGSWV
-GIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSPRKIA
-LTIFNVIIIGIAACICGLGLYVSGRSLHDDANGSSF------------------------
 ------------------------------------------------------------
+---------------------------TCANNAST-------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
----------------------------SCASNA---------------------------
 ------------------------------------------------------------
+>Aspergillus_awamori_IFM_58123|GCB19008.1
+M-----------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
->Aspergillus_awamori_IFM_58123|GCB19337.1
-M--AHPTG----------------------------------------------------
+------------------------APTTRD---LEA----------LAVHHDS-------
+-DIMADDLAEKKVSANESPPENDPFGNEECGEVKYRVMKWWHCGILMIAENISLGILSLP
+SAV---ATLGIVPSIFLILGLSGISWYTGYVIGQFKLRYPQVHSMGDAGEILFGRIGREI
+LFFGQLLFCIFLMSSHILTFTVLFNTITGHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM
+SLASCTSITVATIVTMVAIAVQAPDHVQVDITTHPSFSTAFLSVTNIVFAF---------
+--------IAHVAFFGFASEMEDPRDFPKSLAMLQVTDTTMYIVTAMVIYRYAGPDVASP
+ALSSAGPLMSKVAYGLAIPTVIIAGVVFGHVASKYIYVRVWR-GSPQMHTNSLAAVGSWV
+AIALGVWVIAWIIAESIPVFNDLLSLISSLFGSWFSYGLPAMFWLVMNRGQYTASPRKIF
+LTIVNLVIFGIACAICGLGLYVSGKAIHDSSSSASW------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
-----------------------DKVDSHLN---VQTGQFFQDGREEPYLH----------
-------DAEEKQDEKKGSPIYNDTFGDEEYAEVKYKVLSWWQCGFLMVAETVSLGILSLP
-AVV---ATLGLAPAIVLIVGLGLLATYTGYVIGQFRWRYPHVQNLADAGEILFGSIGREI
-FGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFGVVGLVICFLLGLPRTSANVSYL
-SVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLYEAFLAVCNIVFSF---------
---------SGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGPNVTSP
-ALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFR-HGDRMHSRDLLATGSWV
-GIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSPRKIA
-LTFFNVIIIGIAACICGLGLYVSGRSLHDDANGSSF------------------------
 ------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
----------------------------SCASNA---------------------------
+---------------------------TCANNAST-------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------