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simonhmartin / genomics_general

General tools for genomic analyses.
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popgenWindows.py error #44

Open Andrinajoro opened 3 years ago

Andrinajoro commented 3 years ago

Hi Simon, used popgenWindows.py from your general genomics pakage to estimate diversity and divergence. I was running the following command: python popgenWindows.py -w 50000 -m 5000 -s 50000 --windType coordinate -g all_rename_filter2_geno0_phased_renammed_chr.geno.gz -o all.Fst.Dxy.pi.csv.gz -f phased -T 8 -p ang ang -p bux bux -p der der -p eur eur -p imb imb -p ory ory -p scr scr -p spe spe -p str str -p syl syl

and got the following message: Starting 8 worker threads Traceback (most recent call last): File "popgenWindows.py", line 420, in exclude = scafsToExclude) TypeError: slidingCoordWindows() got an unexpected keyword argument 'headerLine'

I rechecked everithing but could not find out what I am doing wrog. Your advice would be much appreciated Joro

Andrinajoro commented 3 years ago

Hi Simon Could it be a python compatibility issue (currently running python 3.7) or numpy (v 1.19.2)? When running
python2 popgenWindows.py -w 50000 -m 5000 -s 50000 --windType coordinate -g all_rename_filter2_geno0_phased_renammed_chr.geno.gz -o all.Fst.Dxy.pi.csv.gz -f phased -T 8 -p ang ang -p bux bux -p der der -p eur eur -p imb imb -p ory ory -p scr scr -p spe spe -p str str -p syl syl

Traceback (most recent call last): File "popgenWindows.py", line 6, in import numpy as np ImportError: No module named numpy

Joro

simonhmartin commented 3 years ago

Hi Joro, This looks like a bug introduced with the latest version of the script that I uploaded. For now, if you go to the previous version here: https://github.com/simonhmartin/genomics_general/tree/566e04a4d6df9b2dfa0673fdf306ad891564c725 it should hopefully work. I will try to fix the bug when I get a chance. Simon

Andrinajoro commented 3 years ago

Hi Simon, Thanks for your help. Cloned the previous version as you advised and it works fine. Thanks for the awesome packages. Joro

On Fri, Nov 6, 2020 at 11:41 AM Simon martin notifications@github.com wrote:

Hi Joro, This looks like a bug introduced with the latest version of the script that I uploaded. For now, if you go to the previous version here:

https://github.com/simonhmartin/genomics_general/tree/566e04a4d6df9b2dfa0673fdf306ad891564c725 it should hopefully work. I will try to fix the bug when I get a chance. Simon

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/simonhmartin/genomics_general/issues/44#issuecomment-722982222, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARUUUKL5JHOD7Y2D5DOPPRDSOPAFVANCNFSM4TLT3GJQ .

simonhmartin commented 3 years ago

Hi Joro, I just got around to looking for this error, but I don't see a problem in the script. I think the problem might have been that you didn't have the latest version of genomics.py, which was needed to make popgenWindows.py work correctly. If you have a chance to try with the current version, I would be interested to know if it works without error. Thanks, Simon

Andrinajoro commented 3 years ago

Hi Simon Will give it a try and get back to you. Thanks Joro On 16 Nov 2020 23:55, "Simon martin" notifications@github.com wrote:

Hi Joro, I just got around to looking for this error, but I don't see a problem in the script. I think the problem might have been that you didn't have the latest version of genomics.py, which was needed to make popgenWindows.py work correctly. If you have a chance to try with the current version, I would be interested to know if it works without error. Thanks, Simon

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/simonhmartin/genomics_general/issues/44#issuecomment-728352410, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARUUUKKPLE6DETYZ3C3GNWTSQGNWLANCNFSM4TLT3GJQ .