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test_Clustalw
Checking Bio.AlignIO and Bio.Clustalw can read example files...
Testing reading clustal format file Clustalw/cw02.aln with 1 alignments
Using Bio.AlignIO.parse(...)
SingleLetterAlphabet() alignment with 2 rows and 601 columns
MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYR...SVV gi|4959044|gb|AAD34209.1|AF069
---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTD...--- gi|671626|emb|CAA85685.1|
Using Bio.AlignIO.read(...)
Using Bio.Clustalw.parse_file(...)
Testing reading clustal format file Clustalw/opuntia.aln with 1 alignments
Using Bio.AlignIO.parse(...)
SingleLetterAlphabet() alignment with 7 rows and 156 columns
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273291|gb|AF191665.1|AF191
Using Bio.AlignIO.read(...)
Using Bio.Clustalw.parse_file(...)
Testing reading clustal format file Clustalw/protein.aln with 1 alignments
Using Bio.AlignIO.parse(...)
SingleLetterAlphabet() alignment with 20 rows and 411 columns
--------------------------------------------...--- gi|14150838|gb|AAK54648.1|AF37
MTVLEESADASSRRLAQRANGPATVLAIGTANPANVFEQSSYPD...--- gi|12644515|sp|Q9MBB1|CHSY_EQU
------MVTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi|13774971|gb|AAK39113.1|AF35
------MVTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi|13774967|gb|AAK39111.1|AF35
------MVTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi|13774975|gb|AAK39115.1|AF35
------MVTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi|13774965|gb|AAK39110.1|AF35
------MVTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi|13774973|gb|AAK39114.1|AF35
------MVTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi|13774969|gb|AAK39112.1|AF35
-----------------------------------------YPD...--- gi|13919613|gb|AAK33142.1|
-----------------------------------------YPD...--- gi|13919597|gb|AAK33134.1|
------MVTVEEFRRAQCAEGPATVMAIGTATPSNCVDQSTYPD...--- gi|13925890|gb|AAK49457.1|
------MVTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPD...PH- gi|12644514|sp|Q9MB41|CHS2_IPO
------MVTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPD...PH- gi|12644512|sp|Q9MB39|CHS4_IPO
------MVTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPD...--- gi|12644509|sp|Q9MB36|CHS8_IPO
------MVTVEEVRKAQRAEGPATILAIGTATPANCVNQSTYPD...PH- gi|12644511|sp|Q9MB38|CHS6_IPO
------MVTVEEVRKAKRAEGPATILAIGTATPANCVNQSTYPD...PH- gi|12644510|sp|Q9MB37|CHS7_IPO
------MVTVGEVRKAQRAEGPATILAIGTATPANCVNQSTYPD...--- gi|12644513|sp|Q9MB40|CHS3_IPO
----MTSMTVDQIRRPLRAEGLATILAIGTANPANYITQADYPD...--- gi|13936397|dbj|BAB47195.1|
----MTSMTVDQIRRPLRAEGLATILAIGTANPANYITQADYPD...--- gi|13936395|dbj|BAB47194.1|
---MSSSITVDQIRKAQRAEGPATILAIGTATPANFIIQADYPD...SET gi|13936399|dbj|BAB47196.1|
Using Bio.AlignIO.read(...)
Using Bio.Clustalw.parse_file(...)
Testing reading clustal format file Clustalw/odd_consensus.aln with 1 alignments
Using Bio.AlignIO.parse(...)
SingleLetterAlphabet() alignment with 2 rows and 687 columns
--------------------------------------------...TAG AT3G20900.1-CDS
ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGTGAACAAAA...TAG AT3G20900.1-SEQ
Using Bio.AlignIO.read(...)
Using Bio.Clustalw.parse_file(...)
Testing reading clustal format file Clustalw/hedgehog.aln with 1 alignments
Using Bio.AlignIO.parse(...)
SingleLetterAlphabet() alignment with 5 rows and 447 columns
MFNLVSGTGGSSCCHRRNCFANRKKFFTMLLIFLLYMVSQVQSC...--- gi|167877390|gb|EDS40773.1|
---------------------MRSASAAALLLAALLVVQAVRAC...--- gi|167234445|ref|NP_001107837.
-------------MPQR----SLRHQLGMILVFFLLVTSHSLAC...--- gi|74100009|gb|AAZ99217.1|
------------MSPAR----LRPRLHFCLVLLLLLVVPAAWGC...AGS gi|13990994|dbj|BAA33523.2|
----------------------LAADDQGRLLYSDFLTFLDRDD...KSS gi|56122354|gb|AAV74328.1|
Using Bio.AlignIO.read(...)
Using Bio.Clustalw.parse_file(...)
Testing reading clustal format file Clustalw/promals3d.aln with 1 alignments
Using Bio.AlignIO.parse(...)
SingleLetterAlphabet() alignment with 20 rows and 414 columns
M------VTVEEFRRAQCAEGPATVMAIGTATPSNCVDQSTYPD...--- gi_13925890_gb_AAK49457.1
M---SSSITVDQIRKAQRAEGPATILAIGTATPANFIIQADYPD...SET gi_13936399_dbj_BAB47196.
M----TSMTVDQIRRPLRAEGLATILAIGTANPANYITQADYPD...--- gi_13936397_dbj_BAB47195.
M----TSMTVDQIRRPLRAEGLATILAIGTANPANYITQADYPD...--- gi_13936395_dbj_BAB47194.
M------VTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPD...PH- gi_12644514_sp_Q9MB41_CHS
M------VTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPD...PH- gi_12644512_sp_Q9MB39_CHS
M------VTVEEVRKAQRAEGPATILAIGTVTPANCVNQSTYPD...--- gi_12644509_sp_Q9MB36_CHS
M------VTVEEVRKAQRAEGPATILAIGTATPANCVNQSTYPD...PH- gi_12644511_sp_Q9MB38_CHS
M------VTVEEVRKAKRAEGPATILAIGTATPANCVNQSTYPD...PH- gi_12644510_sp_Q9MB37_CHS
M------VTVGEVRKAQRAEGPATILAIGTATPANCVNQSTYPD...--- gi_12644513_sp_Q9MB40_CHS
M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi_13774969_gb_AAK39112.1
M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi_13774971_gb_AAK39113.1
M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi_13774967_gb_AAK39111.1
M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi_13774975_gb_AAK39115.1
M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi_13774965_gb_AAK39110.1
M------VTVEEVRKAQRAEGPATILAIGTATPANCVDQSTYPD...--- gi_13774973_gb_AAK39114.1
--------------------------------------------...--- gi_14150838_gb_AAK54648.1
MTVLEESADASSRRLAQRANGPATVLAIGTANPANVFEQSSYPD...--- gi_12644515_sp_Q9MBB1_CHS
-----------------------------------------YPD...--- gi_13919613_gb_AAK33142.1
-----------------------------------------YPD...--- gi_13919597_gb_AAK33134.1
Using Bio.AlignIO.read(...)
Using Bio.Clustalw.parse_file(...)
Finished tested reading files
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