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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated #57

Closed giuseppe0525 closed 5 years ago

giuseppe0525 commented 6 years ago

Hi,

I got a warning message when I was running DCC and I want to know if the problem would affect the result. The warning is:

/home/admin_g/.local/lib/python2.7/site-packages/DCC-0.4.6-py2.7.egg/DCC/circFilter.py:80: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use arr[tuple(seq)] instead of arr[seq]. In the future this will be interpreted as an array index, arr[np.array(seq)], which will result either in an error or a different result.

In addition, there're many messages in the log file saying

circRNA start position does not have mapped read counts, treated as 0.

I don't know whether these two messages are relevant or not.

I run the command similar to the default:

DCC @samplesheet -mt1 @mate1 -mt2 @mate2 -R [Repeats].gtf -an [Annotation].gtf -Pi -F -M -Nr 1 1 -fg -G -A [Reference].fa

By the way, there's a minor issue when installing DCC if pysam is not installed before. The setup program will download the latest version of pysam, which is 0.15.0, and the installation will be terminated because DCC can not be built under pysam-0.15.0.

Regards, Giuseppe

tjakobi commented 6 years ago

Dear @giuseppe0525,

thank you for reporting the warning. In essence, DCC is using a numpy-package routine that has been marked as deprecated and as of now just produces this warning with no influence on the results. However, this is a piece of code I will have to update in time to make it compatible with the new numpy version.

The start position "read count" message can safely be ignored, I should maybe silence that one at some point and introduce a verbose mode.

Regarding the pysam error, that's somewhat tricky and not directly related to DCC. The HTSeq packages requires an older version of pysam. This error has been fixed in the circtools package but I did not have the time yet to port the fix over to the bare DCC installation.

Thank you, Tobias

giuseppe0525 commented 6 years ago

Thank you Tobias for your explicit answer.