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comprna / SVM-BPfinder

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SVM-BPfinder server failed to be connected #1

Open santataRU opened 4 months ago

santataRU commented 4 months ago

Dear SVM-BPfinder developers,

The SVM-BPfinder server failed (http://regulatorygenomics.upf.edu/Software/SVM_BP/). I tried to connect to the website, but got an error message: "This site can’t be reached, regulatorygenomics.upf.edu refused to connect."

Is this server still open to users?

Thanks,

Xiao

EduEyras commented 4 months ago

Dear Xiao,

sorry about this. The server is not maintained anymore. You can use the code available in the github https://github.com/comprna/SVM-BPfinder It is easy enough to run in the command line. Please let me know if I can help with that. best Eduardo

On Sun, 19 May 2024 at 09:53, xlei @.***> wrote:

Dear SVM-BPfinder developers,

The SVM-BPfinder server failed ( http://regulatorygenomics.upf.edu/Software/SVM_BP/). I tried to connect to the website, but got an error message: "This site can’t be reached, regulatorygenomics.upf.edu refused to connect."

Is this server still open to users?

Thanks,

Xiao

— Reply to this email directly, view it on GitHub https://github.com/comprna/SVM-BPfinder/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB6JJDFYDA56BJ5HS4TZC7SWBAVCNFSM6AAAAABH53DJLKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMYDIMZUG44DGOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

santataRU commented 4 months ago

Dear Eduardo,

Thank you very much! Is the example fasta file (test_A1CF_intron.fa) available so that I can download and test your code?

Best,

Xiao

EduEyras commented 4 months ago

Hi,

yes, it is available in the same GitHub

https://github.com/comprna/SVM-BPfinder/blob/main/test_A1CF_intron.fa

Best

Eduardo

On Sun, 19 May 2024 at 23:36, xlei @.***> wrote:

Dear Eduardo,

Thank you very much! Is the example fasta file (test_A1CF_intron.fa) available so that I can download and test your code?

Best,

Xiao

— Reply to this email directly, view it on GitHub https://github.com/comprna/SVM-BPfinder/issues/1#issuecomment-2119241433, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7KQGOXD6DORHZ3L2LZDCTHJAVCNFSM6AAAAABH53DJLKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJZGI2DCNBTGM . You are receiving this because you commented.Message ID: @.***>

santataRU commented 4 months ago

Thank you very much! I tried but failed with the following message, is this script for python2 (not python3)? : (base) bieniaszlab@Pauls-iMac-2 SVM-BPfinder-main % python svm_bpfinder.py -i test_A1CF_intron.fa -s Hsap -l 100 -d 10

File "/Users/bieniaszlab/Downloads/SVM-BPfinder-main/svm_bpfinder.py", line 63 print '\t'.join(['seq_id','agez','ss_dist','bp_seq','bp_scr','y_cont','ppt_off','ppt_len','ppt_scr','svm_scr']) ^ SyntaxError: invalid syntax

santataRU commented 4 months ago

Even with the correct Python version, another issue with SVM-BPfinder is that it only supports Intel CPUs, not Apple M series CPUs. For Mac OS users with M series CPUs, the hope was the SVM-BPfinder web server, which is no longer available.

EduEyras commented 4 months ago

Thanks for pointing this out. It must be the SVM-light library. I will check whether there is a binary available for the M series or whether we can compile one ourselves. Best Eduardo

On Mon, 27 May 2024 at 11:35, xlei @.***> wrote:

Even with the correct Python version, another issue with SVM-BPfinder is that it only supports Intel CPUs, not Apple M series CPUs. For Mac OS users with M series CPUs, the hope was the SVM-BPfinder web server, which is no longer available.

— Reply to this email directly, view it on GitHub https://github.com/comprna/SVM-BPfinder/issues/1#issuecomment-2132494766, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBZ2AQWVDGDKN6FZODDZEKEWDAVCNFSM6AAAAABH53DJLKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZSGQ4TINZWGY . You are receiving this because you commented.Message ID: @.***>

santataRU commented 4 months ago

Dr. Eyras, Thank you very much!

santataRU commented 3 months ago

Hi Eduardo,

I hope you are doing well. With some effort, I compiled SVM-light for macOS on M series chips. I have also converted the Python 2 scripts to Python 3 scripts using an online converter. Now, SVM-BPfinder can work on the Python 3 platform on Mac computers with M series chips. I have included a link at the end of this email if you would like to download the modified version of SVM-BPfinder. I would not mind if you post the modified version on GitHub for users with macOS on M series chips and those using the Python 3 platform.

Thank you for developing this tool. I am a virologist studying HIV-1 and host RNA splicing, and I am using your SVM-BPfinder tool to score the polypyrimidine tract.

Best regards, Xiao Link: https://drive.google.com/file/d/1M6zohdZasOCXF0CjYrQN6atu8ecHszi1/view?usp=sharing

On Mon, May 27, 2024 at 1:28 AM Eduardo Eyras @.***> wrote:

Thanks for pointing this out. It must be the SVM-light library. I will check whether there is a binary available for the M series or whether we can compile one ourselves. Best Eduardo

On Mon, 27 May 2024 at 11:35, xlei @.***> wrote:

Even with the correct Python version, another issue with SVM-BPfinder is that it only supports Intel CPUs, not Apple M series CPUs. For Mac OS users with M series CPUs, the hope was the SVM-BPfinder web server, which is no longer available.

— Reply to this email directly, view it on GitHub < https://github.com/comprna/SVM-BPfinder/issues/1#issuecomment-2132494766>,

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EduEyras commented 3 months ago

Thanks a lot Xiao This is really wonderful! I'll put it in the github, perhaps a separate repository to make things more clear. If you don't mind, I will add a thank you to https://github.com/santataRU or in any way you prefer Best Eduardo

On Tue, 2 Jul 2024 at 05:11, xlei @.***> wrote:

Hi Eduardo,

I hope you are doing well. With some effort, I compiled SVM-light for macOS on M series chips. I have also converted the Python 2 scripts to Python 3 scripts using an online converter. Now, SVM-BPfinder can work on the Python 3 platform on Mac computers with M series chips. I have included a link at the end of this email if you would like to download the modified version of SVM-BPfinder. I would not mind if you post the modified version on GitHub for users with macOS on M series chips and those using the Python 3 platform.

Thank you for developing this tool. I am a virologist studying HIV-1 and host RNA splicing, and I am using your SVM-BPfinder tool to score the polypyrimidine tract.

Best regards, Xiao Link:

https://drive.google.com/file/d/1M6zohdZasOCXF0CjYrQN6atu8ecHszi1/view?usp=sharing

On Mon, May 27, 2024 at 1:28 AM Eduardo Eyras @.***> wrote:

Thanks for pointing this out. It must be the SVM-light library. I will check whether there is a binary available for the M series or whether we can compile one ourselves. Best Eduardo

On Mon, 27 May 2024 at 11:35, xlei @.***> wrote:

Even with the correct Python version, another issue with SVM-BPfinder is that it only supports Intel CPUs, not Apple M series CPUs. For Mac OS users with M series CPUs, the hope was the SVM-BPfinder web server, which is no longer available.

— Reply to this email directly, view it on GitHub < https://github.com/comprna/SVM-BPfinder/issues/1#issuecomment-2132494766>,

or unsubscribe <

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santataRU commented 3 months ago

Hi Eduardo,

Thank you for your kindness. I am fine with adding a thank you to https://github.com/santataRU.

Best regards,

Xiao

On Tue, Jul 2, 2024 at 7:33 AM Eduardo Eyras @.***> wrote:

Thanks a lot Xiao This is really wonderful! I'll put it in the github, perhaps a separate repository to make things more clear. If you don't mind, I will add a thank you to https://github.com/santataRU or in any way you prefer Best Eduardo

On Tue, 2 Jul 2024 at 05:11, xlei @.***> wrote:

Hi Eduardo,

I hope you are doing well. With some effort, I compiled SVM-light for macOS on M series chips. I have also converted the Python 2 scripts to Python 3 scripts using an online converter. Now, SVM-BPfinder can work on the Python 3 platform on Mac computers with M series chips. I have included a link at the end of this email if you would like to download the modified version of SVM-BPfinder. I would not mind if you post the modified version on GitHub for users with macOS on M series chips and those using the Python 3 platform.

Thank you for developing this tool. I am a virologist studying HIV-1 and host RNA splicing, and I am using your SVM-BPfinder tool to score the polypyrimidine tract.

Best regards, Xiao Link:

https://drive.google.com/file/d/1M6zohdZasOCXF0CjYrQN6atu8ecHszi1/view?usp=sharing

On Mon, May 27, 2024 at 1:28 AM Eduardo Eyras @.***> wrote:

Thanks for pointing this out. It must be the SVM-light library. I will check whether there is a binary available for the M series or whether we can compile one ourselves. Best Eduardo

On Mon, 27 May 2024 at 11:35, xlei @.***> wrote:

Even with the correct Python version, another issue with SVM-BPfinder is that it only supports Intel CPUs, not Apple M series CPUs. For Mac OS users with M series CPUs, the hope was the SVM-BPfinder web server, which is no longer available.

— Reply to this email directly, view it on GitHub <

https://github.com/comprna/SVM-BPfinder/issues/1#issuecomment-2132494766>,

or unsubscribe <

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