new installation of miniconda I run into this error

[Hasanzahid10]

ImportError Traceback (most recent call last)
Cell In[23], line 4
2 path='show'
3 test_path=("data1/densiflorus (plastid)- MT740250.1 retained.fasta")
----> 4 BCAWT_auto_test.auto_test(path,test_path)
5 BCAWT_auto_test.auto_check_file(path)

File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT_auto_test.py:24, in auto_test(path, test_file)
21 from BCAWT import BCAWT
22 file = open(test_file, "r")
---> 24 BCAWT.BCAW(main_fasta_file = [file] , save_path= path, Auto=True)

File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT.py:34, in BCAW(main_fasta_file, save_path, ref_fasta_file, genetic_code_, Auto)
32 #from Bio.Alphabet import IUPAC
33 from Bio.Seq import Seq
---> 34 from Bio.SeqUtils import GC
35 from Bio.Data import CodonTable
36 #from Bio.Alphabet import generic_dna

ImportError: cannot import name 'GC' from 'Bio.SeqUtils' (/home/u1/miniconda3/lib/python3.11/site-packages/Bio/SeqUtils/init.py)

[Hasanzahid10]

Hello sir,
'I am run Staphylococcus_aureus.fasta in your codonU tools but there is show different result. why and how to solve it's,
I am new users. I am share two ss you.one ss your GitHub output. one is mine

![Screenshot from 2024-05-13 17-27-14] (https://github.com/linxingchen/cobra/assets/143874164/522dc511-3ecd-4a52-9bf5-bb0dae1d524b)
![Screenshot from 2024-05-13 17-27-30] (https://github.com/linxingchen/cobra/assets/143874164/1090c5c3-a98e-4846-8897-3d8a24c64aa9)

[linxingchen]

ImportError Traceback (most recent call last) Cell In[23], line 4 2 path='show' 3 test_path=("data1/densiflorus (plastid)- MT740250.1 retained.fasta") ----> 4 BCAWT_auto_test.auto_test(path,test_path) 5 BCAWT_auto_test.auto_check_file(path)

File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT_auto_test.py:24, in auto_test(path, test_file) 21 from BCAWT import BCAWT 22 file = open(test_file, "r") ---> 24 BCAWT.BCAW(main_fasta_file = [file] , save_path= path, Auto=True)

File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT.py:34, in BCAW(main_fasta_file, save_path, ref_fasta_file, genetic_code_, Auto) 32 #from Bio.Alphabet import IUPAC 33 from Bio.Seq import Seq ---> 34 from Bio.SeqUtils import GC 35 from Bio.Data import CodonTable 36 #from Bio.Alphabet import generic_dna

ImportError: cannot import name 'GC' from 'Bio.SeqUtils' (/home/u1/miniconda3/lib/python3.11/site-packages/Bio/SeqUtils/init.py)

Hi,
Sorry for my delayed reply. I think the issue is due to an older version of Bio. Could you please update it to the newest one and try it again?

Best,
LINXING

[linxingchen]

Hello sir, 'I am run Staphylococcus_aureus.fasta in your codonU tools but there is show different result. why and how to solve it's, I am new users. I am share two ss you.one ss your GitHub output. one is mine

![Screenshot from 2024-05-13 17-27-14] (https://github.com/linxingchen/cobra/assets/143874164/522dc511-3ecd-4a52-9bf5-bb0dae1d524b) ![Screenshot from 2024-05-13 17-27-30] (https://github.com/linxingchen/cobra/assets/143874164/1090c5c3-a98e-4846-8897-3d8a24c64aa9)

Hi, I am confused because I have never developed any tools for codon usage frequency calculation. Could you please clarify which one you were using? Thanks.

[Hasanzahid10]

thank you...for your replying But.... I am use biopython 1.83 same problem... After that i found there GC function missing..... And i add this function solve this problem. But i am face new issue.... Scipy...issue.....

…

On Sat, 18 May, 2024, 5:45 pm LinXing Chen, ***@***.***> wrote: ImportError Traceback (most recent call last) Cell In[23], line 4 2 path='show' 3 test_path=("data1/densiflorus (plastid)- MT740250.1 retained.fasta") ----> 4 BCAWT_auto_test.auto_test(path,test_path) 5 BCAWT_auto_test.auto_check_file(path) File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT_auto_test.py:24, in auto_test(path, test_file) 21 from BCAWT import BCAWT 22 file = open(test_file, "r") ---> 24 BCAWT.BCAW(main_fasta_file = [file] , save_path= path, Auto=True) File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT.py:34, in BCAW(main_fasta_file, save_path, ref_fasta_file, genetic_code_, Auto) 32 #from Bio.Alphabet import IUPAC 33 from Bio.Seq import Seq ---> 34 from Bio.SeqUtils import GC 35 from Bio.Data import CodonTable 36 #from Bio.Alphabet import generic_dna ImportError: cannot import name 'GC' from 'Bio.SeqUtils' (/home/u1/miniconda3/lib/python3.11/site-packages/Bio/SeqUtils/*init*.py) Hi, Sorry for my delayed reply. I think the issue is due to an older version of Bio. Could you please update it to the newest one and try it again? Best, LINXING — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BCJVQ5DXMCJ3TM653LW4QFTZC4PKPAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42DIMBQGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[linxingchen]

thank you...for your replying But.... I am use biopython 1.83 same problem... After that i found there GC function missing..... And i add this function solve this problem. But i am face new issue.... Scipy...issue.....
…
On Sat, 18 May, 2024, 5:45 pm LinXing Chen, @.> wrote: ImportError Traceback (most recent call last) Cell In[23], line 4 2 path='show' 3 test_path=("data1/densiflorus (plastid)- MT740250.1 retained.fasta") ----> 4 BCAWT_auto_test.auto_test(path,test_path) 5 BCAWT_auto_test.auto_check_file(path) File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT_auto_test.py:24, in auto_test(path, test_file) 21 from BCAWT import BCAWT 22 file = open(test_file, "r") ---> 24 BCAWT.BCAW(main_fasta_file = [file] , save_path= path, Auto=True) File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT.py:34, in BCAW(main_fasta_file, save_path, ref_fasta_file, genetic_code_, Auto) 32 #from Bio.Alphabet import IUPAC 33 from Bio.Seq import Seq ---> 34 from Bio.SeqUtils import GC 35 from Bio.Data import CodonTable 36 #from Bio.Alphabet import generic_dna ImportError: cannot import name 'GC' from 'Bio.SeqUtils' (/home/u1/miniconda3/lib/python3.11/site-packages/Bio/SeqUtils/init.py) Hi, Sorry for my delayed reply. I think the issue is due to an older version of Bio. Could you please update it to the newest one and try it again? Best, LINXING — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCJVQ5DXMCJ3TM653LW4QFTZC4PKPAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42DIMBQGI . You are receiving this because you authored the thread.Message ID: @.>

Sorry to hear that. Have you updated COBRA to the newest version, which actually resolved the GC issue.

what is your new issue please?

[Hasanzahid10]

Fixed! On Sat, 18 May, 2024, 5:53 pm LinXing Chen, ***@***.***> wrote:

…

thank you...for your replying But.... I am use biopython 1.83 same problem... After that i found there GC function missing..... And i add this function solve this problem. But i am face new issue.... Scipy...issue..... … <#m_8160598087212029592_> On Sat, 18 May, 2024, 5:45 pm LinXing Chen, *@*.*> wrote: ImportError Traceback (most recent call last) Cell In[23], line 4 2 path='show' 3 test_path=("data1/densiflorus (plastid)- MT740250.1 retained.fasta") ----> 4 BCAWT_auto_test.auto_test(path,test_path) 5 BCAWT_auto_test.auto_check_file(path) File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT_auto_test.py:24, in auto_test(path, test_file) 21 from BCAWT import BCAWT 22 file = open(test_file, "r") ---> 24 BCAWT.BCAW(main_fasta_file = [file] , save_path= path, Auto=True) File ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT.py:34, in BCAW(main_fasta_file, save_path, ref_fasta_file, genetic_code_, Auto) 32 #from Bio.Alphabet import IUPAC 33 from Bio.Seq import Seq ---> 34 from Bio.SeqUtils import GC 35 from Bio.Data import CodonTable 36 #from Bio.Alphabet import generic_dna ImportError: cannot import name 'GC' from 'Bio.SeqUtils' (/home/u1/miniconda3/lib/python3.11/site-packages/Bio/SeqUtils/init.py) Hi, Sorry for my delayed reply. I think the issue is due to an older version of Bio. Could you please update it to the newest one and try it again? Best, LINXING — Reply to this email directly, view it on GitHub <#36 (comment) <#36 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCJVQ5DXMCJ3TM653LW4QFTZC4PKPAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42DIMBQGI <https://github.com/notifications/unsubscribe-auth/BCJVQ5DXMCJ3TM653LW4QFTZC4PKPAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42DIMBQGI> . You are receiving this because you authored the thread.Message ID: @.*> Sorry to hear that. Have you updated COBRA to the newest version, which actually resolved the GC issue. what is your new issue please? — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BCJVQ5GSB6KG5XTLXQMB6ALZC4QLFAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42TANRXGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[linxingchen]

Glad to hear it! Lin-xing Chen Postdoc of the Banfield lab Earth and Planetary Science University of California, Berkeley Berkeley, CA, USA Hasanzahid10 ***@***.***> 于2024年5月18日周六 18:12写道：

…

Fixed! On Sat, 18 May, 2024, 5:53 pm LinXing Chen, ***@***.***> wrote: > thank you...for your replying But.... I am use biopython 1.83 same > problem... After that i found there GC function missing..... And i add this > function solve this problem. But i am face new issue.... Scipy...issue..... > … <#m_8160598087212029592_> > On Sat, 18 May, 2024, 5:45 pm LinXing Chen, *@*.*> wrote: ImportError > Traceback (most recent call last) Cell In[23], line 4 2 path='show' 3 > test_path=("data1/densiflorus (plastid)- MT740250.1 retained.fasta") ----> > 4 BCAWT_auto_test.auto_test(path,test_path) 5 > BCAWT_auto_test.auto_check_file(path) File > ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT_auto_test.py:24, in > auto_test(path, test_file) 21 from BCAWT import BCAWT 22 file = > open(test_file, "r") ---> 24 BCAWT.BCAW(main_fasta_file = [file] , > save_path= path, Auto=True) File > ~/miniconda3/lib/python3.11/site-packages/BCAWT/BCAWT.py:34, in > BCAW(main_fasta_file, save_path, ref_fasta_file, genetic_code_, Auto) 32 > #from Bio.Alphabet import IUPAC 33 from Bio.Seq import Seq ---> 34 from > Bio.SeqUtils import GC 35 from Bio.Data import CodonTable 36 #from > Bio.Alphabet import generic_dna ImportError: cannot import name 'GC' from > 'Bio.SeqUtils' > (/home/u1/miniconda3/lib/python3.11/site-packages/Bio/SeqUtils/init.py) Hi, > Sorry for my delayed reply. I think the issue is due to an older version of > Bio. Could you please update it to the newest one and try it again? Best, > LINXING — Reply to this email directly, view it on GitHub <#36 (comment) > <#36 (comment)>>, > or unsubscribe > https://github.com/notifications/unsubscribe-auth/BCJVQ5DXMCJ3TM653LW4QFTZC4PKPAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42DIMBQGI > < https://github.com/notifications/unsubscribe-auth/BCJVQ5DXMCJ3TM653LW4QFTZC4PKPAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42DIMBQGI> > . You are receiving this because you authored the thread.Message ID: @.*> > > Sorry to hear that. Have you updated COBRA to the newest version, which > actually resolved the GC issue. > > what is your new issue please? > > — > Reply to this email directly, view it on GitHub > <#36 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/BCJVQ5GSB6KG5XTLXQMB6ALZC4QLFAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42TANRXGM> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALEPRGPBJRGUCSJBEKLQ6ZLZC4SQ7AVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG43DANBXGI> . You are receiving this because you commented.Message ID: ***@***.***>