NameError: global name 'sort' is not defined

[Tinalxt]

Hi~ I had the same problem metioned in #30, but when I run the example_data with version 0.0.6, I got a new problem, just like below:
1 Traceback (most recent call last):
2 File "/Workspace/home/difanglei/pipeline/ctDNA/software/BreaKmer-0.0.6/breakmer.py", line 96, in
3 r.run(tic)
4 File "/Workspace/home/difanglei/pipeline/ctDNA/software/BreaKmer-0.0.6/sv_processor.py", line 189, in run
5 trgt.extract_bam_reads() # Extract the reads that provide evidence for structural variation.
6 File "/Workspace/home/difanglei/pipeline/ctDNA/software/BreaKmer-0.0.6/sv_processor.py", line 537, in extract_bam_reads
7 sort(self.files['sv_bam'],self.files['sv_bam_sorted'].replace('.bam',''))
8 NameError: global name 'sort' is not defined
I wonder if it is a new bug? And how can I fix it. Thank you~

[GuillaumeMEXP]

Hi,

I get the same error, did you manage to solve it ?

Thanks !

[ryanabo]

Hello! Sorry about the troubles. This error is new to me (as the main developer) and I am wondering what version of python you are using.

[ryanabo]

Please try my branched version - https://github.com/ryanabo/BreaKmer

[GuillaumeMEXP]

Dear Ryan, Thanks a lot for your answer ! I am using python 2.7.6. Pysam and Biopython are uptodate. I tried to run your Master branch but I still get an error when I prepare the data : guillaume@guillaume-linux[venvs] python /home/guillaume/Downloads/BreaKmer-master/breakmer.py prepare_reference_data -c /home/guillaume/Documents/breakmer_test_master.cfg Traceback (most recent call last): File "/home/guillaume/Downloads/BreaKmer-master/breakmer.py", line 72, in <module> PMANAGER = params.ParamManager(PARSER.parse_args()) File "/home/guillaume/Downloads/BreaKmer-master/breakmer/params.py", line 49, in __init__ self.set_params() File "/home/guillaume/Downloads/BreaKmer-master/breakmer/params.py", line 114, in set_params self.set_insertsize_thresh() # Set the expected insert size threshold from the properly mapped read File "/home/guillaume/Downloads/BreaKmer-master/breakmer/params.py", line 327, in set_insertsize_thresh insertsize_sd = utils.stddev(utils.remove_outliers(insert_sizes)) # Calculate the standard deviation of the sample read pairs insert sizes. File "/home/guillaume/Downloads/BreaKmer-master/breakmer/utils.py", line 810, in remove_outliers intv_cut = 1.5 * (qnt2 - qnt1) TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType' Do you have any idea on how to fix this problem ? Thank you so much ! Have a nice day Will

…

________________________________ De : Ryan Abo <[email protected]> Envoyé : jeudi 7 décembre 2017 21:09:12 À : ccgd-profile/BreaKmer Cc : Guillaume Dachy; Comment Objet : Re: [ccgd-profile/BreaKmer] NameError: global name 'sort' is not defined (#34) Please try my branched version - https://github.com/ryanabo/BreaKmer — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#34 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AglKnR4RvRF0gLQ6LgdCK9Ik7d4-RWb9ks5s-EXngaJpZM4Mn9Qs>.

[ryanabo]

Hi Will,

I will address this here but would appreciate if you posted the issue in the repo from which the code was downloaded. I don't get notices on this repo anymore so I could easily miss your issues. As for your current issue, I am suspecting your bam is not being read properly. Can you copy and paste a handful of the sequence reads from the bam file that are aligned? This could easily be a formatting issue and my code is not robust to it, but should be an easy fix.

Ryan

[GuillaumeMEXP]

Hi, I made a new issue in the repo of your Master branch ryanabo#2 There is a link to a bam file to test. Cheers [https://avatars2.githubusercontent.com/u/34163357?s=400&v=4]<https://github.com/ryanabo/BreaKmer/issues/2> error prepare_reference_data · Issue #2 · ryanabo/BreaKmer<ryanabo#2> github.com Hi, First, thanks Ryan for this very interesting software and for the help you provide ! I tried to run your Master branch but I still get an error when I prepare the data : I am using python 2.7.6...

…

________________________________ De : Ryan Abo <[email protected]> Envoyé : vendredi 8 décembre 2017 22:04:40 À : ccgd-profile/BreaKmer Cc : Guillaume Dachy; Comment Objet : Re: [ccgd-profile/BreaKmer] NameError: global name 'sort' is not defined (#34) Hi Will, I will address this here but would appreciate if you posted the issue in the repo from which the code was downloaded. I don't get notices on this repo anymore so I could easily miss your issues. As for your current issue, I am suspecting your bam is not being read properly. Can you copy and paste a handful of the sequence reads from the bam file that are aligned? This could easily be a formatting issue and my code is not robust to it, but should be an easy fix. Ryan — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#34 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AglKnXmj9TbD4chu4ZXiDCmQblWHDrmHks5s-aRngaJpZM4Mn9Qs>.

[Myno-Jeong]

Hi.

I also had the same problem with Tinalxt.
1 Traceback (most recent call last):
2 File "/Workspace/home/difanglei/pipeline/ctDNA/software/BreaKmer-0.0.6/breakmer.py", line 96, in
3 r.run(tic)
4 File "/Workspace/home/difanglei/pipeline/ctDNA/software/BreaKmer-0.0.6/sv_processor.py", line 189, in run
5 trgt.extract_bam_reads() # Extract the reads that provide evidence for structural variation.
6 File "/Workspace/home/difanglei/pipeline/ctDNA/software/BreaKmer-0.0.6/sv_processor.py", line 537, in extract_bam_reads
7 sort(self.files['sv_bam'],self.files['sv_bam_sorted'].replace('.bam',''))
8 NameError: global name 'sort' is not defined
I sorted my bam file using gatk SortSam module.

I couldn't solve this problem.
I used BreakMer version 0.0.7 and python 2.7.6.

Would you let me know how I can solve this problem?

Many thanks,