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initial testing of new python and biopython versions
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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118 changes: 59 additions & 59 deletions
118
tests/samples/OG0000010.renamed.fa.mafft.clipkit.orthosnap.4.fa
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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------------------------- | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ | ||
| ------------------------------------------------------------ |