diff --git a/.DS_Store b/.DS_Store index 4a92185e..3c76d7fa 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/requirements.txt b/requirements.txt index 49a2f044..813e6160 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,14 @@ -biopython==1.78 -numpy==1.20.1 -tqdm==4.58.0 \ No newline at end of file +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 diff --git a/setup.py b/setup.py index c6fed529..641d0470 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ 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 diff --git a/tests/samples/OG0000010.renamed.fa.mafft.clipkit.orthosnap.4.fa b/tests/samples/OG0000010.renamed.fa.mafft.clipkit.orthosnap.4.fa index d432845e..4111a72e 100644 --- a/tests/samples/OG0000010.renamed.fa.mafft.clipkit.orthosnap.4.fa +++ b/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------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------