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christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation
MIT License
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error with GC_skew #9

Closed BJCampbelllab closed 6 years ago

BJCampbelllab commented 7 years ago

Hi- I'm new to iRep, but am really eager to use it and see my results! I get this error when I run gc_skew: -bash-4.2$ gc_skew -f CB_Spr15_L08_bin.56.fa File "/usr/bin/gc_skew", line 49 print('%s: Too Short' % (name), file=sys.stderr) ^ SyntaxError: invalid syntax

Any help/suggestions would be appreciated!

BJCampbelllab commented 7 years ago

Okay, I see that the program needs matlab. I don't have it (it is expensive, I believe). Any workaround for that?

christophertbrown commented 7 years ago

Hi,

iRep does not require Matlab or any software that needs to be purchased. It looks to me like you were trying to run gc_skew with python 2.7 instead of python 3. I recommend using pyenv to install python 3 and to manage different python versions.

Hope this helps!

Chris

On Jun 4, 2017, at 9:41 AM, BJCampbelllab notifications@github.com wrote:

Okay, I see that the program needs matlab. I don't have it (it is expensive, I believe). Any workaround for that?

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On Jun 4, 2017, at 8:25 AM, BJCampbelllab notifications@github.com wrote:

Hi- I'm new to iRep, but am really eager to use it and see my results! I get this error when I run gc_skew: -bash-4.2$ gc_skew -f CB_Spr15_L08_bin.56.fa File "/usr/bin/gc_skew", line 49 print('%s: Too Short' % (name), file=sys.stderr) ^ SyntaxError: invalid syntax

Any help/suggestions would be appreciated!

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BJCampbelllab commented 7 years ago

Thanks! I'll let you know if I have any more issues.

Sent from my iPhone

On Jun 5, 2017, at 12:56 PM, christophertbrown notifications@github.com<mailto:notifications@github.com> wrote:

Hi,

iRep does not require Matlab or any software that needs to be purchased. It looks to me like you were trying to run gc_skew with python 2.7 instead of python 3. I recommend using pyenv to install python 3 and to manage different python versions.

Hope this helps!

Chris

On Jun 4, 2017, at 9:41 AM, BJCampbelllab notifications@github.com<mailto:notifications@github.com> wrote:

Okay, I see that the program needs matlab. I don't have it (it is expensive, I believe). Any workaround for that?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

On Jun 4, 2017, at 8:25 AM, BJCampbelllab notifications@github.com<mailto:notifications@github.com> wrote:

Hi- I'm new to iRep, but am really eager to use it and see my results! I get this error when I run gc_skew: -bash-4.2$ gc_skew -f CB_Spr15_L08_bin.56.fa File "/usr/bin/gc_skew", line 49 print('%s: Too Short' % (name), file=sys.stderr) ^ SyntaxError: invalid syntax

Any help/suggestions would be appreciated!

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