Python3 Incompatibilities

[apeltzer]

So apparently there are quite some issues with Python3+, making reading input files quite difficult.

a.) UTF-8/Latin-1 file encodings are quite difficult to handle in Python3, especially forcing these to be consistent on how input reading was handled automatically by Python 2.

cf for details:

https://stackoverflow.com/questions/12468179/unicodedecodeerror-utf8-codec-cant-decode-byte-0x9c

b.) I guess the easiest way would be adding pysam (which is installable via python-pip, conda etc pp) and then rely on this as reading/writing library for SAM/BAM compatibility. One could even have automatic MD tagging activated, making the process easier for users too.

[pontussk]

Hi Alex, This would be great but one of the goals I have had for PMDtools has been to have minimal dependencies (only samtools in principle). Is there any possibility other than pysam for this? Best, Pontus

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On Sat, Nov 3, 2018 at 6:27 PM Alexander Peltzer ***@***.***> wrote: So apparently there are quite some issues with Python3+, making reading input files quite difficult. a.) UTF-8/Latin-1 file encodings are quite difficult to handle in Python3, especially forcing these to be consistent on how input reading was handled automatically by Python 2. cf for details: https://stackoverflow.com/questions/12468179/unicodedecodeerror-utf8-codec-cant-decode-byte-0x9c b.) I guess the easiest way would be adding pysam (which is installable via python-pip, conda etc pp) and then rely on this as reading/writing library for SAM/BAM compatibility. One could even have automatic MD tagging activated, making the process easier for users too. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF3_IyKcbQjw2KWZNq2KDECAxoxE_dbzks5ureAVgaJpZM4YM7zd> .

[apeltzer]

Hi Pontus,

yes, we could work on fixing these issues in the code directly - @boulund apparently ported the code basis to Python3 without changing that, so we could ask him again whether he can share what he changed :-)

cf nf-core/eager#36

[boulund]

I haven't had time to look at this in detail, maybe my code has the same issue with encodings as you've encountered?

Please have a look at the start of the rewrite I made here: https://github.com/boulund/PMDtools/tree/boulund-rewrite

Note that I made my rewrite of this a while back, before the code was put online under a permissive license, so if there are recent changes they are probably not incorporated in my version of the code.

[pontussk]

Thanks Fredrik that is interesting.

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On Thu, Nov 8, 2018 at 12:43 PM Fredrik Boulund ***@***.***> wrote: I haven't had time to look at this in detail, maybe my code has the same issue with encodings as you've encountered? Please have a look at the rewrite I made here: https://github.com/boulund/PMDtools/tree/boulund-rewrite Note that I made my rewrite of this a while back, before the code was put online under a permissive license. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AF3_I55ys43q6kNem6M2yWx6iPFW2Sq1ks5utCcIgaJpZM4YM7zd> .

[rsh249]

Was there a solution to the python3 incompatibility?

[apeltzer]

None that I'm aware of unfortunately so far. I#ve not had time to have a more detailed look but would be happy to see such an update :-)

[boulund]

I haven't compared the results from my python3 conversion with the original code, but it runs in python 3 and produces reasonably looking output.

[rsh249]

I made an attempt to make the original script work with python3 and also get sensible results (so far).

https://github.com/rsh249/PMDtools *cloned repository with fixes for python3

I’ll check out yours @boulund too!

[apeltzer]

If this works reliably, could be a good thing to open a PR to this repository and get it updated in a new release maybe ?

[rsh249]

I will keep testing and let you know if my version seems OK for a PR. Thanks all!

[pontussk]

Thanks all for looking at porting this to python3. Let me know what I can do. Pontus

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On Mon, 1 Feb 2021 at 01:59, Rob Harbert ***@***.***> wrote: I will keep testing and let you know if my version seems OK for a PR. Thanks all! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO76I2HAQJF37X4WQQXRXTS4YDHHANCNFSM4GBTXTOQ> .

[boulund]

Is there still interest in a Python3 port of PMDtools ?
If there are any significant updates to the original code of version 0.6 (which is labelled 0.5 in the code) I could add them to my py3 port and create a PR to this repo, if anyone still wants it. Maybe PMDtools is good enough as is, or people have moved on to something else?
Is there a good test data set that could be used to verify that the output doesn't change?

[pontussk]

Hi Fredrik, I would certainly be interested in this. Thanks! Best, Pontus

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On Mon, 5 Sept 2022 at 15:11, Fredrik Boulund ***@***.***> wrote: Is there still interest in a Python3 port of PMDtools ? If there are any significant updates to the original code of version 0.6 (which is labelled 0.5 in the code) I could add them to my py3 port and create a PR to this repo, if anyone still wants it. Maybe people have moved on to something else? — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO76I62E37G667BZYRKZNTV4X5P5ANCNFSM4GBTXTOQ> . You are receiving this because you commented.Message ID: ***@***.***>