https://sourceforge.net/p/conifer/activity/Recent activity for CoNIFERenWed, 27 Oct 2021 04:43:30 -0000https://sourceforge.net/p/conifer/discussion/general/thread/440fc6fbf9/?limit=25#54b2python 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 syntaxDhwani DholakiaWed, 27 Oct 2021 04:43:30 -0000https://sourceforge.net/p/conifer/discussion/general/thread/440fc6fbf9/?limit=25#54b2https://sourceforge.net/p/conifer/discussion/general/thread/440fc6fbf9/?limit=25#54b2python 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 syntaxDhwani DholakiaWed, 27 Oct 2021 04:43:16 -0000https://sourceforge.net/p/conifer/discussion/general/thread/440fc6fbf9/?limit=25#54b2https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#306bYout 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.htmlZiyun DingMon, 04 Nov 2019 18:27:12 -0000https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#306bhttps://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#bc86Hi Virginie, I have the same problem, did you perhaps find the solution? All the best, MarijaMarija BrankovicWed, 12 Dec 2018 14:50:16 -0000https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#bc86https://sourceforge.net/p/conifer/discussion/general/thread/d874b756/?limit=25#f131Hi 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.kumarafmWed, 04 Jul 2018 14:55:11 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d874b756/?limit=25#f131https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#8116this code is as old as greek's piramides. now it should be f.check_index()Damian LoskaWed, 06 Jun 2018 17:40:10 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#8116https://sourceforge.net/p/conifer/discussion/general/thread/02b3285f/?limit=25#d14fHi, 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 KrithikaKrithikaTue, 02 Jan 2018 12:19:57 -0000https://sourceforge.net/p/conifer/discussion/general/thread/02b3285f/?limit=25#d14fhttps://sourceforge.net/p/conifer/discussion/general/thread/7aa1f519/?limit=25#fc59Hi, Have you tried these solutions? https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/ simonzee anwer worked for me. Regards.Manuel Solís MorunoWed, 11 Oct 2017 15:19:59 -0000https://sourceforge.net/p/conifer/discussion/general/thread/7aa1f519/?limit=25#fc59https://sourceforge.net/p/conifer/discussion/general/thread/02b3285f/?limit=25#4fc1Hi, 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...Manuel Solís MorunoWed, 11 Oct 2017 13:49:28 -0000https://sourceforge.net/p/conifer/discussion/general/thread/02b3285f/?limit=25#4fc1https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#fc8fHi, 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, VirginieVirginie CHESNAISMon, 10 Jul 2017 07:47:36 -0000https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#fc8fhttps://sourceforge.net/p/conifer/discussion/general/thread/c54ced22/?limit=25#1aceHi, Can you tell me how (or if) the use of duplicate marked BAMS would affect the result? Thanks! AledAled MorrisMon, 05 Jun 2017 16:55:01 -0000https://sourceforge.net/p/conifer/discussion/general/thread/c54ced22/?limit=25#1acehttps://sourceforge.net/p/conifer/discussion/general/thread/7aa1f519/?limit=25#22d5Hi I am new in the field of bioinformatics. I have recently installed conifer for...MilenaWed, 12 Apr 2017 10:32:23 -0000https://sourceforge.net/p/conifer/discussion/general/thread/7aa1f519/?limit=25#22d5https://sourceforge.net/p/conifer/discussion/general/thread/7aa1f519/?limit=25#22d5Hi I am new in the field of bioinformatics. I have recently installed conifer for...MilenaWed, 12 Apr 2017 10:22:36 -0000https://sourceforge.net/p/conifer/discussion/general/thread/7aa1f519/?limit=25#22d5https://sourceforge.net/p/conifer/discussion/general/thread/9325da69/?limit=25#39d8/3a2cI don’t think this is an error with the tables installation. What commands did you...Niklas KrummFri, 31 Mar 2017 00:08:50 -0000https://sourceforge.net/p/conifer/discussion/general/thread/9325da69/?limit=25#39d8/3a2chttps://sourceforge.net/p/conifer/discussion/general/thread/9325da69/?limit=25#39d8Hello, I'm running python 2.7, tables 2.3 (i also tried 2.3.1), numpy 1.5.1, numexpr...JP TsaiThu, 30 Mar 2017 19:12:46 -0000https://sourceforge.net/p/conifer/discussion/general/thread/9325da69/?limit=25#39d8https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#8b3c/f9e6/1b94Thank you very much for your fast and helpful answer. It was indeed the version of...Elodie DarboFri, 03 Mar 2017 06:50:09 -0000https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#8b3c/f9e6/1b94https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#8b3c/f9e6Hi Elodie, I believe that PyTables has been updated version 3 has breaking API changes...Niklas KrummFri, 03 Mar 2017 04:58:09 -0000https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#8b3c/f9e6https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#8b3cDear CoNIFER developers, I am very interested in using CoNIFER. I am using python...Elodie DarboThu, 02 Mar 2017 10:46:07 -0000https://sourceforge.net/p/conifer/discussion/general/thread/0ec5cd75/?limit=25#8b3chttps://sourceforge.net/p/conifer/discussion/general/thread/69034009/?limit=25#1f3cI'm trying to use conifer and I'm stuck on this error: conifer.py:617: RuntimeWarning:...Andrey LeonardoMon, 13 Feb 2017 14:34:34 -0000https://sourceforge.net/p/conifer/discussion/general/thread/69034009/?limit=25#1f3chttps://sourceforge.net/p/conifer/discussion/general/thread/ea913614/?limit=25#8642Hello, can somebody please help me? I try to run python conifer.py analyze --probes...Sri DewiWed, 08 Jun 2016 10:52:21 -0000https://sourceforge.net/p/conifer/discussion/general/thread/ea913614/?limit=25#8642https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#5da8Hi all, I ran into the same issue and simonzee's suggestion didn't work for me. I...Tim WebsterFri, 03 Jun 2016 23:36:08 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#5da8https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#7d93It's a very simple fix. Just change line 564 of conifer.py from: if not f._hasIndex():...simonzeeThu, 28 Apr 2016 23:13:36 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#7d93https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#3461I'm having the same problem too. Still no fix? python conifer.py rpkm \ --probes...Stuart TompsonTue, 02 Feb 2016 23:51:15 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#3461https://sourceforge.net/p/conifer/discussion/general/thread/abe157b2/?limit=25#56c8/87f8/376bI'm running this on a Ubuntu 12.04 64bit, on a virtual machine running on Windows...zhenjiang lanMon, 01 Feb 2016 16:52:53 -0000https://sourceforge.net/p/conifer/discussion/general/thread/abe157b2/?limit=25#56c8/87f8/376bhttps://sourceforge.net/p/conifer/discussion/general/thread/abe157b2/?limit=25#56c8/87f8Hi-- I've never seen this error before. From the looks of it is something with the...Niklas KrummSat, 30 Jan 2016 20:00:32 -0000https://sourceforge.net/p/conifer/discussion/general/thread/abe157b2/?limit=25#56c8/87f8https://sourceforge.net/p/conifer/discussion/general/thread/abe157b2/?limit=25#56c8Hi, I'm newly using Conifier. I'm trying to make it work. when I tried to do the...zhenjiang lanFri, 29 Jan 2016 17:48:51 -0000https://sourceforge.net/p/conifer/discussion/general/thread/abe157b2/?limit=25#56c8https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#74a2Hello David, I'm having the exact same problem, did you solved?. the same error was...Eduardo PerezSat, 12 Dec 2015 00:21:27 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#74a2https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#2f3cHello, you made very good tool, I am new user of CoNIFER and I try to run conifer.py...David StanekWed, 25 Nov 2015 13:21:19 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#2f3chttps://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#2f3cHello, you made very good tool, I am new user of CoNIFER and I try to run conifer.py...David StanekWed, 25 Nov 2015 13:20:56 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#2f3chttps://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#2f3cHello, you made very good tool, I am new user of CoNIFER and I try to run conifer.py...David StanekWed, 25 Nov 2015 13:20:39 -0000https://sourceforge.net/p/conifer/discussion/general/thread/d2fbc181/?limit=25#2f3chttps://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#ca42/9f4cHi Katy, This ones totally benign actually-- just that you have a zero length exon...Niklas KrummTue, 23 Jun 2015 05:30:16 -0000https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#ca42/9f4chttps://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#ca42Hi Niklas, I have another question, when I generate my RPKM files I get the following...KattysTue, 23 Jun 2015 04:35:37 -0000https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#ca42https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#91a8/79b9/cb1bHi Niklas!!! Thanks a lot, I had a problem with the file name and I was sorting the...KattysFri, 22 May 2015 17:43:57 -0000https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#91a8/79b9/cb1bhttps://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#91a8/79b9Hi Katy, This is a new one to me. I’m wondering if you have a version of samtools...Niklas KrummTue, 28 Apr 2015 15:58:32 -0000https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#91a8/79b9https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#91a8/6648Hi Katy, This is a new one to me. I’m wondering if you have a version of samtools...Niklas KrummTue, 28 Apr 2015 15:52:59 -0000https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#91a8/6648https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#91a8Hello, Thank you for made CONIFER available, I am trying to run python conifer.py...Katy Sanchez-PozosTue, 28 Apr 2015 15:16:08 -0000https://sourceforge.net/p/conifer/discussion/general/thread/9bc0fa8a/?limit=25#91a8https://sourceforge.net/p/conifer/discussion/general/thread/484069f3/?limit=25#fd2bHi, I am having issues with Conifer plotting the call images. It manages for about...aligTue, 07 Apr 2015 00:47:19 -0000https://sourceforge.net/p/conifer/discussion/general/thread/484069f3/?limit=25#fd2bhttps://sourceforge.net/p/conifer/discussion/general/thread/27055199/?limit=25#6b85Hi all, After a long time I used conifer again and now I'm struggling against a simple...daweonlineThu, 23 Jan 2014 15:12:55 -0000https://sourceforge.net/p/conifer/discussion/general/thread/27055199/?limit=25#6b85