new installation of miniconda I run into this error #36
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Hello sir, ![Screenshot from 2024-05-13 17-27-14] (https://github.com/linxingchen/cobra/assets/143874164/522dc511-3ecd-4a52-9bf5-bb0dae1d524b) |
Hi, Best, |
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. |
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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
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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? |
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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)
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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?
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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
>
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> <
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> . 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)>,
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> You are receiving this because you authored the thread.Message ID:
> ***@***.***>
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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)
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