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linxingchen / cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
MIT License
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new installation of miniconda I run into this error #36

Open Hasanzahid10 opened 4 months ago

Hasanzahid10 commented 4 months ago

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, geneticcode, 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 commented 4 months ago

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 commented 4 months ago

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, geneticcode, 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 commented 4 months ago

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 commented 4 months ago

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, geneticcode, 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 https://github.com/linxingchen/cobra/issues/36#issuecomment-2118744002, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCJVQ5DXMCJ3TM653LW4QFTZC4PKPAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42DIMBQGI . You are receiving this because you authored the thread.Message ID: @.***>

linxingchen commented 4 months ago

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, geneticcode, 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 commented 4 months ago

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..... … <#m8160598087212029592> 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, geneticcode, 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) https://github.com/linxingchen/cobra/issues/36#issuecomment-2118744002>, 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 https://github.com/linxingchen/cobra/issues/36#issuecomment-2118750673, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCJVQ5GSB6KG5XTLXQMB6ALZC4QLFAVCNFSM6AAAAABHBUM426VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYG42TANRXGM . You are receiving this because you authored the thread.Message ID: @.***>

linxingchen commented 4 months ago

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..... … <#m8160598087212029592> 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, geneticcode, 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) https://github.com/linxingchen/cobra/issues/36#issuecomment-2118744002>,

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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 https://github.com/linxingchen/cobra/issues/36#issuecomment-2118750673,

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