CoNIFER Activity
Homepage for CoNIFER (Copy Number Inference From Exome Reads)
Status: Beta
Brought to you by:
nkrumm99
Activity for CoNIFER
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Dhwani Dholakia modified a comment on discussion General Discussion
python conifer.py rpkm --probes ../probes.txt --input ../208A_S37.bam --output sample.txt File "/conifer_v0.2.1/conifer.py", line 43 print '[INIT] Successfully read in %d probes from %s' % (num_probes, probe_fn) ^ SyntaxError: invalid syntax
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python conifer.py rpkm --probes ../probes.txt --input ../VUR208A_S37.bam --output sample.txt File "/conifer_v0.2.1/conifer.py", line 43 print '[INIT] Successfully read in %d probes from %s' % (num_probes, probe_fn) ^ SyntaxError: invalid syntax
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Ziyun Ding posted a comment on discussion General Discussion
Yout don't need to downgrade to pytable version 2. You can refer to this webpage to change the function names to version 3. For example "openFile" to "open_file" https://www.pytables.org/MIGRATING_TO_3.x.html
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Marija Brankovic posted a comment on discussion General Discussion
Hi Virginie, I have the same problem, did you perhaps find the solution? All the best, Marija
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kumarafm posted a comment on discussion General Discussion
Hi all, I am generating RPKM from my bam files (I have solved the issue regarding the index file changing the conifer.py code) however the script finds a very low number or reads ranging from 1 to 9 when there should be an enormous amount instead. Does someone have the same problem? I think this is causing problems when executing the "analyze" command, where I get an error regarding numpy.
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Damian Loska posted a comment on discussion General Discussion
this code is as old as greek's piramides. now it should be f.check_index()
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Krithika posted a comment on discussion General Discussion
Hi, I too have the same issue. I get the same error when I try to actually call CNVs. The previous steps worked fine. Were you able to find a solution to this issue? Thanks Krithika
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Manuel Solís Moruno posted a comment on discussion General Discussion
Hi, Have you tried these solutions? https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/ simonzee anwer worked for me. Regards.
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Hi, I'm using CoNIFER v0.2.2 with Python 2.7.13, PyTables 2.4.0 and PySam 0.8.3. I managed to create the RPKM files for my 5 samples and I also created the corresponding files using the command analyze. Here you have what I executed: python $conifer rpkm --probes $probes --input $input/BQSR_S${i}.bam --output $input/BQSR_S${i}.rpkm.txt mv $input/BQSR_S${i}.rpkm.txt $RPKMs python $conifer analyze --probes $probes --rpkm_dir $RPKMs --output $results/analysis_BQSR_S${i}.hdf5 --svd 4 --write_svals $results/singular_values_BQSR_S${i}.txt...
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Virginie CHESNAIS posted a comment on discussion General Discussion
Hi, I have the same issue than Elodie and try to downgraded PyTables but I have lots of dependancies troubles. Is that very impossible to use your software with pytables v2? Or do you have a procedure to help me to install pytables v2? Thanks Best regards, Virginie
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Aled Morris posted a comment on discussion General Discussion
Hi, Can you tell me how (or if) the use of duplicate marked BAMS would affect the result? Thanks! Aled
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Milena modified a comment on discussion General Discussion
Hi I am new in the field of bioinformatics. I have recently installed conifer for...
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Hi I am new in the field of bioinformatics. I have recently installed conifer for...
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Niklas Krumm posted a comment on discussion General Discussion
I don’t think this is an error with the tables installation. What commands did you...
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JP Tsai posted a comment on discussion General Discussion
Hello, I'm running python 2.7, tables 2.3 (i also tried 2.3.1), numpy 1.5.1, numexpr...
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Elodie Darbo posted a comment on discussion General Discussion
Thank you very much for your fast and helpful answer. It was indeed the version of...
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Hi Elodie, I believe that PyTables has been updated version 3 has breaking API changes...
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Dear CoNIFER developers, I am very interested in using CoNIFER. I am using python...
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Andrey Leonardo posted a comment on discussion General Discussion
I'm trying to use conifer and I'm stuck on this error: conifer.py:617: RuntimeWarning:...
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Sri Dewi posted a comment on discussion General Discussion
Hello, can somebody please help me? I try to run python conifer.py analyze --probes...
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Tim Webster posted a comment on discussion General Discussion
Hi all, I ran into the same issue and simonzee's suggestion didn't work for me. I...
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simonzee posted a comment on discussion General Discussion
It's a very simple fix. Just change line 564 of conifer.py from: if not f._hasIndex():...
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Stuart Tompson posted a comment on discussion General Discussion
I'm having the same problem too. Still no fix? python conifer.py rpkm \ --probes...
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zhenjiang lan posted a comment on discussion General Discussion
I'm running this on a Ubuntu 12.04 64bit, on a virtual machine running on Windows...
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Hi-- I've never seen this error before. From the looks of it is something with the...
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Hi, I'm newly using Conifier. I'm trying to make it work. when I tried to do the...
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Eduardo Perez posted a comment on discussion General Discussion
Hello David, I'm having the exact same problem, did you solved?. the same error was...
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David Stanek modified a comment on discussion General Discussion
Hello, you made very good tool, I am new user of CoNIFER and I try to run conifer.py...
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Hello, you made very good tool, I am new user of CoNIFER and I try to run conifer.py...
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Hello, you made very good tool, I am new user of CoNIFER and I try to run conifer.py...
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Hi Katy, This ones totally benign actually-- just that you have a zero length exon...
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Kattys posted a comment on discussion General Discussion
Hi Niklas, I have another question, when I generate my RPKM files I get the following...
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Hi Niklas!!! Thanks a lot, I had a problem with the file name and I was sorting the...
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Hi Katy, This is a new one to me. I’m wondering if you have a version of samtools...
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Hi Katy, This is a new one to me. I’m wondering if you have a version of samtools...
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Hello, Thank you for made CONIFER available, I am trying to run python conifer.py...
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alig posted a comment on discussion General Discussion
Hi, I am having issues with Conifer plotting the call images. It manages for about...
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daweonline posted a comment on discussion General Discussion
Hi all, After a long time I used conifer again and now I'm struggling against a simple...
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