Genome bed file

[kr-colab]

Genome bed file

[jradrion]

I think it's an issue with either the column separator or the newline separator you are using in that file. The code is just trying to split each line on whitespace using .split() to get the chromosome, start position, and end postion. Can you send your .bed file so I can take a look? Either that or just reformat the file so that it can be split on whitespace.

I have attached an example for the first line in your example above

genome_file.txt

[tanu06]

Hello, Thank You so much. I made a tab separated file in notepad. Please find the attached in email. I thought my chromosome number has some problem. Thank You, Tanu

On Thu, Apr 23, 2020 at 7:42 PM Jeffrey Adrion ***@***.***> wrote: I think it's an issue with either the column separator or the newline separator you are using in that file. The code is just trying to split each line on whitespace using .split() to get the chromosome, start position, and end postion. Can you send your .bed file so I can take a look? Either that or just reformat the file so that it can be split on whitespace. I have attached an example for the first line in your example above genome_file.txt <https://github.com/kern-lab/ReLERNN/files/4525854/genome_file.txt> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE7BZCTQ4OVRYDBHAZNY6D3RODG7ZANCNFSM4MOWQ7AQ> .

CM009931.2 0 27754200 CM009932.2 0 16093500 CM009933.2 0 13619445 CM009934.2 0 13404451 CM009935.2 0 13920984 CM009936.2 0 17812983 CM009937.2 0 14262382 CM009938.2 0 12786769 CM009939.2 0 12729961 CM009940.2 0 12657134 CM009941.2 0 16444887 CM009942.2 0 11533137 CM009943.2 0 11279722 CM009944.2 0 10910039 CM009945.2 0 9922473 CM009946.2 0 7238532

[jradrion]

I didn't receive a file attachment, can you double check that you sent it? Also, I'm not sure what end-of-line character notepad uses, but my guess is that it might be \r\n and not \n. If that is the case you could probably remedy this by using a different text editor.

[tanu06]

Hello, I checked and it looks like its \n. Please find the attached file. Thank you, Tanushree

On Fri, Apr 24, 2020 at 6:28 PM Jeffrey Adrion ***@***.***> wrote: I didn't receive a file attachment, can you double check that you sent it? Also, I'm not sure what end-of-line character notepad uses, but my guess is that it might be \r\n and not \n. If that is the case you could probably remedy this by using a different text editor. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE7BZCTJWX7XBTWCWBFHASLROIHA3ANCNFSM4MOWQ7AQ> .

CM009931.2 0 27754200 CM009932.2 0 16093500 CM009933.2 0 13619445 CM009934.2 0 13404451 CM009935.2 0 13920984 CM009936.2 0 17812983 CM009937.2 0 14262382 CM009938.2 0 12786769 CM009939.2 0 12729961 CM009940.2 0 12657134 CM009941.2 0 16444887 CM009942.2 0 11533137 CM009943.2 0 11279722 CM009944.2 0 10910039 CM009945.2 0 9922473 CM009946.2 0 7238532

[jradrion]

I still have not receive an attached file. If the scaffolds currently printed to the screen above are the ones you want to run ReLERNN on, use the following genome file:
genome_file.txt

[tanu06]

Hello, Thank you so much. I really appreciate your help. Thank You, Tanushree

…

On Mon, Apr 27, 2020 at 11:52 AM Jeffrey Adrion ***@***.***> wrote: I still have not receive an *attached* file. If the scaffolds currently printed to the screen above are the ones you want to run ReLERNN you can use this genome file: genome_file.txt <https://github.com/kern-lab/ReLERNN/files/4540669/genome_file.txt> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE7BZCULYIYCP2SAJC7AC6DROWS2NANCNFSM4MOWQ7AQ> .

[tanu06]

Hello, While running ReLERNN_PREDICT_POOL i am getting this error, is there a way i can get around it or I have to rename my chromosomes ? File "/home/tanu06/project/tanu06/ReLERNN/ReLERNN/ReLERNN_PREDICT_POOL", line 142, in <module> main() File "/home/tanu06/project/tanu06/ReLERNN/ReLERNN/ReLERNN_PREDICT_POOL", line 113, in main gpuID=args.gpuID) File "/project/6002169/tanu06/ReLERNN/ReLERNN/ReLERNN/helpers.py", line 292, in load_and_predictVCF last = int(os.path.basename(resultsFile).split(".")[0].split("-")[-1]) ValueError: invalid literal for int() with base 10: 'CM009931' Thank You, Tanushree On Mon, Apr 27, 2020 at 2:01 PM tanushree tiwari <[email protected]> wrote:

…

Hello, Thank you so much. I really appreciate your help. Thank You, Tanushree On Mon, Apr 27, 2020 at 11:52 AM Jeffrey Adrion ***@***.***> wrote: > I still have not receive an *attached* file. If the scaffolds currently > printed to the screen above are the ones you want to run ReLERNN you can > use this genome file: > genome_file.txt > <https://github.com/kern-lab/ReLERNN/files/4540669/genome_file.txt> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#18 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AE7BZCULYIYCP2SAJC7AC6DROWS2NANCNFSM4MOWQ7AQ> > . >

[tanu06]

Hello,
I got it working, it was chromosome name that was giving me error.
What would you suggest for his parameter, --nReps NREPS for pooled data.

Thank you for all your help and prompt responses.
Thank you,
Tanushree

[jradrion]

Hi, there was a bug in how we were handling some chromosome names, which should be fixed now. Changing the names should have fixed the issue as well.

What would you suggest for his parameter, --nReps NREPS for pooled data.

using the defaults for both --nReps and --nSlice should be fine

[tanu06]

Thank You, Yes changing the names of chromosomes helped and i used defaults for both. Your paper has so cool graphs for recombination rates/MB. Is there any review article which can help me understand my results better because original one is too technical for me to understand. I really appreciate all your help and time. Thank You, Tanushree

…

On Wed, Apr 29, 2020 at 7:24 PM Jeffrey Adrion ***@***.***> wrote: Hi, there was a bug in how we were handling some chromosome names, which should be fixed now. Changing the names should have fixed the issue as well. What would you suggest for his parameter, --nReps NREPS for pooled data. using the defaults for both --nReps and --nSlice should be fine — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE7BZCTIVYLTFRQULKKDSPTRPCZKRANCNFSM4MOWQ7AQ> .