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beliveau-lab / OligoMiner

Genome-scale design tool for oligo hybridization probes
MIT License
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blcokParse.py: AttributeError #10

Closed gang237 closed 4 years ago

gang237 commented 4 years ago

Hello, Prof. Beliveau, I have met a problem when running blockParse.py file, and it seems that something is wrong with the script file, because I also met this error when using the example fasta file downloaded from the website.

This is the error information: Traceback (most recent call last): File "blockParse.py", line 993, in main() File "blockParse.py", line 981, in main exec ('nn_table = mt.%s' % args.nn_table) File "", line 1, in AttributeError: 'module' object has no attribute 'DNA_NN3'

It would be very nice of you if you can help me with this problem! Thank you so much!

brianbeliveau commented 4 years ago

Hello,

We have seen this error before, and in the past it was related to issues with the Biopython install. Can you please verify you can use the MeltingTemp module in your Python environment as in these examples: https://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-module.html ?

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Tue, Jun 9, 2020 at 2:24 AM gang237 notifications@github.com wrote:

Hello, Prof. Beliveau, I have met a problem when running blockParse.py file, and it seems that something is wrong with the script file, because I also met this error when using the example fasta file downloaded from the website.

This is the error information: Traceback (most recent call last): File "blockParse.py", line 993, in main() File "blockParse.py", line 981, in main exec ('nn_table = mt.%s' % args.nn_table) File "", line 1, in AttributeError: 'module' object has no attribute 'DNA_NN3'

It would be very nice of you if you can help me with this problem! Thank you so much!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/beliveau-lab/OligoMiner/issues/10, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHIXQ2UJCXGI4PDKREW6LFTRVX5UNANCNFSM4NZG6ROA .

gang237 commented 4 years ago

Hello, Prof. Beliveau, I re-installed my biopython-1.76, and it works now!

Thank you so much!

gang237 commented 4 years ago

Dear Professor Beliveau,

my name is Gang Wu. I have successfully run the blockparse script and got the fasta output file after I re-installed biopython. Thank you so much!

While I have met with another problem, I can not open the webiste for downloading nupack3.0.4. Do you have an alternative website for this?

Best wishes!

Brian J. Beliveau notifications@github.com 于2020年6月10日周三 上午12:33写道：

Hello,

We have seen this error before, and in the past it was related to issues with the Biopython install. Can you please verify you can use the MeltingTemp module in your Python environment as in these examples: https://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-module.html ?

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Tue, Jun 9, 2020 at 2:24 AM gang237 notifications@github.com wrote:

Hello, Prof. Beliveau, I have met a problem when running blockParse.py file, and it seems that something is wrong with the script file, because I also met this error when using the example fasta file downloaded from the website.

This is the error information: Traceback (most recent call last): File "blockParse.py", line 993, in main() File "blockParse.py", line 981, in main exec ('nn_table = mt.%s' % args.nn_table) File "", line 1, in AttributeError: 'module' object has no attribute 'DNA_NN3'

It would be very nice of you if you can help me with this problem! Thank you so much!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/beliveau-lab/OligoMiner/issues/10, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AHIXQ2UJCXGI4PDKREW6LFTRVX5UNANCNFSM4NZG6ROA

.

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brianbeliveau commented 4 years ago

Try this. You will need to register: http://www.nupack.org/downloads/register

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Wed, Jun 10, 2020 at 3:59 AM gang237 notifications@github.com wrote:

Dear Professor Beliveau,

my name is Gang Wu. I have successfully run the blockparse script and got the fasta output file after I re-installed biopython. Thank you so much!

While I have met with another problem, I can not open the webiste for downloading nupack3.0.4. Do you have an alternative website for this?

Best wishes!

Brian J. Beliveau notifications@github.com 于2020年6月10日周三 上午12:33写道：

Hello,

We have seen this error before, and in the past it was related to issues with the Biopython install. Can you please verify you can use the MeltingTemp module in your Python environment as in these examples: https://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-module.html ?

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Tue, Jun 9, 2020 at 2:24 AM gang237 notifications@github.com wrote:

Hello, Prof. Beliveau, I have met a problem when running blockParse.py file, and it seems that something is wrong with the script file, because I also met this error when using the example fasta file downloaded from the website.

This is the error information: Traceback (most recent call last): File "blockParse.py", line 993, in main() File "blockParse.py", line 981, in main exec ('nn_table = mt.%s' % args.nn_table) File "", line 1, in AttributeError: 'module' object has no attribute 'DNA_NN3'

It would be very nice of you if you can help me with this problem! Thank you so much!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/beliveau-lab/OligoMiner/issues/10, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AHIXQ2UJCXGI4PDKREW6LFTRVX5UNANCNFSM4NZG6ROA

.

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gang237 commented 4 years ago

Dear Professor Beliveau,

thank you so much! But I could not open this link. I am now in China, and I think there might be some kind of restrictions to foreign requests due to political reasons.

I will try to find some other websites.

Thank you so much for your help! And hope everything goes well in U.S.A. God bless.

Best regards!

Brian J. Beliveau notifications@github.com 于2020年6月10日周三 下午9:48写道：

Try this. You will need to register: http://www.nupack.org/downloads/register

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Wed, Jun 10, 2020 at 3:59 AM gang237 notifications@github.com wrote:

Dear Professor Beliveau,

my name is Gang Wu. I have successfully run the blockparse script and got the fasta output file after I re-installed biopython. Thank you so much!

While I have met with another problem, I can not open the webiste for downloading nupack3.0.4. Do you have an alternative website for this?

Best wishes!

Brian J. Beliveau notifications@github.com 于2020年6月10日周三 上午12:33写道：

Hello,

We have seen this error before, and in the past it was related to issues with the Biopython install. Can you please verify you can use the MeltingTemp module in your Python environment as in these examples:

https://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-module.html ?

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Tue, Jun 9, 2020 at 2:24 AM gang237 notifications@github.com wrote:

Hello, Prof. Beliveau, I have met a problem when running blockParse.py file, and it seems that something is wrong with the script file, because I also met this error when using the example fasta file downloaded from the website.

This is the error information: Traceback (most recent call last): File "blockParse.py", line 993, in main() File "blockParse.py", line 981, in main exec ('nn_table = mt.%s' % args.nn_table) File "", line 1, in AttributeError: 'module' object has no attribute 'DNA_NN3'

It would be very nice of you if you can help me with this problem! Thank you so much!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/beliveau-lab/OligoMiner/issues/10, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AHIXQ2UJCXGI4PDKREW6LFTRVX5UNANCNFSM4NZG6ROA

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— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

https://github.com/beliveau-lab/OligoMiner/issues/10#issuecomment-641418827

, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AP4U55KYA5LVKTCORXW2FJ3RVZP7JANCNFSM4NZG6ROA

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brianbeliveau commented 4 years ago

Ah, you will need to contact the NUPACK developers directly in that case.

For what it's worth, we do not routinely run structureCheck as part of our probe design pipeline, as it is computationally expensive and most probes do not have significant secondary structure potential under FISH conditions.

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Wed, Jun 10, 2020 at 7:03 PM gang237 notifications@github.com wrote:

Dear Professor Beliveau,

thank you so much! But I could not open this link. I am now in China, and I think there might be some kind of restrictions to foreign requests due to political reasons.

I will try to find some other websites.

Thank you so much for your help! And hope everything goes well in U.S.A. God bless.

Best regards!

Brian J. Beliveau notifications@github.com 于2020年6月10日周三 下午9:48写道：

Try this. You will need to register: http://www.nupack.org/downloads/register

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Wed, Jun 10, 2020 at 3:59 AM gang237 notifications@github.com wrote:

Dear Professor Beliveau,

my name is Gang Wu. I have successfully run the blockparse script and got the fasta output file after I re-installed biopython. Thank you so much!

While I have met with another problem, I can not open the webiste for downloading nupack3.0.4. Do you have an alternative website for this?

Best wishes!

Brian J. Beliveau notifications@github.com 于2020年6月10日周三 上午12:33写道：

Hello,

We have seen this error before, and in the past it was related to issues with the Biopython install. Can you please verify you can use the MeltingTemp module in your Python environment as in these examples:

https://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-module.html ?

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Tue, Jun 9, 2020 at 2:24 AM gang237 notifications@github.com wrote:

Hello, Prof. Beliveau, I have met a problem when running blockParse.py file, and it seems that something is wrong with the script file, because I also met this error when using the example fasta file downloaded from the website.

This is the error information: Traceback (most recent call last): File "blockParse.py", line 993, in main() File "blockParse.py", line 981, in main exec ('nn_table = mt.%s' % args.nn_table) File "", line 1, in AttributeError: 'module' object has no attribute 'DNA_NN3'

It would be very nice of you if you can help me with this problem! Thank you so much!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/beliveau-lab/OligoMiner/issues/10, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AHIXQ2UJCXGI4PDKREW6LFTRVX5UNANCNFSM4NZG6ROA

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

https://github.com/beliveau-lab/OligoMiner/issues/10#issuecomment-641418827

, or unsubscribe <

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gang237 commented 4 years ago

Dear Professor Beliveau,

thank you for your suggestions. I will try to contact the developers.

Best wishes!

Brian J. Beliveau notifications@github.com 于2020年6月11日周四 下午10:11写道：

Ah, you will need to contact the NUPACK developers directly in that case.

For what it's worth, we do not routinely run structureCheck as part of our probe design pipeline, as it is computationally expensive and most probes do not have significant secondary structure potential under FISH conditions.

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Wed, Jun 10, 2020 at 7:03 PM gang237 notifications@github.com wrote:

Dear Professor Beliveau,

thank you so much! But I could not open this link. I am now in China, and I think there might be some kind of restrictions to foreign requests due to political reasons.

I will try to find some other websites.

Thank you so much for your help! And hope everything goes well in U.S.A. God bless.

Best regards!

Brian J. Beliveau notifications@github.com 于2020年6月10日周三 下午9:48写道：

Try this. You will need to register: http://www.nupack.org/downloads/register

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Wed, Jun 10, 2020 at 3:59 AM gang237 notifications@github.com wrote:

Dear Professor Beliveau,

my name is Gang Wu. I have successfully run the blockparse script and got the fasta output file after I re-installed biopython. Thank you so much!

While I have met with another problem, I can not open the webiste for downloading nupack3.0.4. Do you have an alternative website for this?

Best wishes!

Brian J. Beliveau notifications@github.com 于2020年6月10日周三 上午12:33写道：

Hello,

We have seen this error before, and in the past it was related to issues with the Biopython install. Can you please verify you can use the MeltingTemp module in your Python environment as in these examples:

https://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-module.html

?

Brian J. Beliveau, Ph.D. Assistant Professor of Genome Sciences University of Washington He/him/his +1 978-390-1933 | beliveau.io

On Tue, Jun 9, 2020 at 2:24 AM gang237 notifications@github.com wrote:

Hello, Prof. Beliveau, I have met a problem when running blockParse.py file, and it seems that something is wrong with the script file, because I also met this error when using the example fasta file downloaded from the website.

This is the error information: Traceback (most recent call last): File "blockParse.py", line 993, in main() File "blockParse.py", line 981, in main exec ('nn_table = mt.%s' % args.nn_table) File "", line 1, in AttributeError: 'module' object has no attribute 'DNA_NN3'

It would be very nice of you if you can help me with this problem! Thank you so much!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/beliveau-lab/OligoMiner/issues/10, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AHIXQ2UJCXGI4PDKREW6LFTRVX5UNANCNFSM4NZG6ROA

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— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

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