Closed ofleitas closed 9 months ago
firasmidani
commented
9 months ago There may be something wrong with your meta.txt file. In the meta.txt file, you should have only one row for each unique Plate_ID. Is that the case? If not, please share here or via e-mail and I can help troubleshoot.
ofleitas
commented
9 months ago Hello
I am attaching the meta.txt file. Thank very much for your help.
On Thu, Dec 7, 2023 at 9:57 AM Firas Midani @.***> wrote:
There may be something wrong with your meta.txt file. In the meta.txt file, you should have only one row for each unique Plate_ID. Is that case? If not, please share here or via e-mail and I can try to help troubleshoot.
— Reply to this email directly, view it on GitHub https://github.com/firasmidani/amiga/issues/20#issuecomment-1845603407, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM624NATNXSAXWUTCZ2DDJDYIHRO7AVCNFSM6AAAAABADWJ3Y2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBVGYYDGNBQG4 . You are receiving this because you authored the thread.Message ID: @.***>
Plate_ID Isolate Comments Group ControlB2 Plate_1 U3 Resistant 1 0 B3 Plate_1 U4 Resistant 1 0 B4 Plate_1 U5 Resistant 1 0 B5 Plate_1 U6 Parental 1 1 B6 Plate_1 U7 Sensitive 1 0 C2 Plate_2 U3 Resistant 1 0 C3 Plate_2 U4 Resistant 1 0 C4 Plate_2 U5 Resistant 1 0 C5 Plate_2 U6 Parental 1 1 C6 Plate_2 U7 Sensitive 1 0 D2 Plate_3 U3 Resistant 1 0 D3 Plate_3 U4 Resistant 1 0 D4 Plate_3 U5 Resistant 1 0 D5 Plate_3 U6 Parental 1 1 D6 Plate_3 U7 Sensitive 1 0 E2 Plate_4 U3 Resistant 1 0 E3 Plate_4 U4 Resistant 1 0 E4 Plate_4 U5 Resistant 1 0 E5 Plate_4 U6 Parental 1 1 E6 Plate_4 U7 Sensitive 1 0 F2 Plate_5 U3 Resistant 1 0 F3 Plate_5 U4 Resistant 1 0 F4 Plate_5 U5 Resistant 1 0 F5 Plate_5 U6 Parental 1 1 F6 Plate_5 U7 Sensitive 1 0
firasmidani
commented
9 months ago To fix this, you simply need to create a separate mapping file for each plate. I see that you have five plates. So, you should have five mapping files in the mapping folder, for example, with the following names:
mapping/Plate_1.txt
mapping/Plate_2.txt
mapping/Plate_3.txt
mapping/Plate_4.txt
mapping/Plate_5.txt
Each mapping file should only describe wells for its corresponding plate. Make sure that the mapping files have the same name as the data files. So, the above names would work if your data folder has the following files:
data/Plate_1.txt
data/Plate_2.txt
data/Plate_3.txt
data/Plate_4.txt
data/Plate_5.txt
A meta.txt file would not work for your case. Revisit the section "How to use a meta.txt file?" in Metadata Doc for more information. I will have to revise the docs to make this point a bit clearer. However, I may keep this issue open, because it would be nice if a user can define mapping for multiples plates in the same file as you have done here. I will add this to the list of improvements to make AMiGA.
Please try the above fix and let me know if it works.
ofleitas
commented
9 months ago It worked. However, when I executed the fit command, I get the following error:
Temporary directory is C:\Users\ofm83\AppData\Local\Temp\tmpmdawzyx6
Fitting Plate_1
Fitting Plate_1 B2
Traceback (most recent call last):
File "amiga.py", line 400, in
firasmidani
commented
9 months ago I can't tell what's happening just from the error. I would like to reproduce the error on my side. Can you share at least one of the data and mapping file combinations?
ofleitas
commented
9 months ago Follow the files
On Mon, Dec 11, 2023 at 1:03 PM Firas Midani @.***> wrote:
I can't tell what's happening just from the error. I would like to reproduce the error on my side. Can you share at least one of the data and mapping file combinations?
— Reply to this email directly, view it on GitHub https://github.com/firasmidani/amiga/issues/20#issuecomment-1850704950, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM624NBBHSXCAII573BCIUTYI5KGJAVCNFSM6AAAAABADWJ3Y2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJQG4YDIOJVGA . You are receiving this because you authored the thread.Message ID: @.***>
0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 8 8.5 9 9.5 10 10.5 11 11.5 12 12.5 13 13.5 14 14.5 15 15.5 16 16.5 17 17.5 18 18.5 19 19.5 20 20.5 21 21.5 22 22.5 23 23.5 24B2 0.000333333 0.002333333 0.005 0.003666667 0.012 0.022666667 0.034333333 0.055333333 0.064 0.076666667 0.09 0.104333333 0.115 0.123333333 0.133 0.142666667 0.160333333 0.163 0.17 0.181 0.172 0.186333333 0.185333333 0.187666667 0.189333333 0.193666667 0.196666667 0.195333333 0.197666667 0.197666667 0.197333333 0.197 0.191333333 0.187333333 0.184666667 0.181666667 0.177666667 0.172666667 0.169 0.165666667 0.161 0.154 0.151333333 0.144666667 0.130666667 0.125333333 0.122333333 0.106 0.097666667 B3 0.002666667 0.004333333 0.007333333 0.005 0.01 0.016333333 0.021666667 0.038333333 0.05 0.057333333 0.07 0.083 0.095666667 0.105 0.115333333 0.124666667 0.139666667 0.146 0.157333333 0.164333333 0.176666667 0.176333333 0.197 0.231333333 0.25 0.268666667 0.277 0.29 0.296333333 0.298 0.303 0.326 0.341 0.374333333 0.398 0.398666667 0.435666667 0.467333333 0.462333333 0.414666667 0.438666667 0.421 0.417 0.449333333 0.419 0.428 0.453333333 0.428 0.421333333 B4 0.002666667 0.004333333 0.006333333 0.002666667 0.007333333 0.012 0.02 0.038333333 0.048333333 0.057666667 0.072666667 0.084 0.102 0.115666667 0.130666667 0.141333333 0.148 0.164 0.166666667 0.176666667 0.195666667 0.201666667 0.229 0.274333333 0.3 0.335666667 0.370333333 0.363333333 0.378 0.388666667 0.391 0.406 0.431333333 0.436333333 0.454333333 0.41 0.340333333 0.310333333 0.235666667 0.237333333 0.237333333 0.234666667 0.237 0.239333333 0.239333333 0.240666667 0.243 0.244333333 0.244666667 B5 0.001 0.004 0.008 0.006333333 0.016666667 0.033 0.050333333 0.068666667 0.073666667 0.097666667 0.109333333 0.126666667 0.148333333 0.160666667 0.171666667 0.182333333 0.190333333 0.197666667 0.203666667 0.210333333 0.216 0.222666667 0.224333333 0.228 0.232666667 0.232333333 0.229333333 0.224 0.224 0.216666667 0.216333333 0.210333333 0.201666667 0.197 0.193333333 0.189 0.177666667 0.178333333 0.169333333 0.161666667 0.168666667 0.151333333 0.145666667 0.141666667 0.125333333 0.126333333 0.104333333 0.095333333 0.086 B6 0.003333333 0.006666667 0.013333333 0.013 0.020333333 0.037 0.059666667 0.083666667 0.100333333 0.121333333 0.136666667 0.169666667 0.196 0.248333333 0.285666667 0.305666667 0.338 0.373 0.404333333 0.455333333 0.477333333 0.535666667 0.536666667 0.592666667 0.61 0.665 0.683333333 0.719333333 0.738666667 0.748333333 0.774666667 0.793333333 0.768333333 0.758333333 0.752 0.747 0.690666667 0.738 0.694666667 0.694 0.651666667 0.663666667 0.689333333 0.732333333 0.711333333 0.707666667 0.642666667 0.631333333 0.581
firasmidani
commented
9 months ago I was able to run both amiga summarize and fit commands successfully on the data that you shared.
So, what was the actual command that you used which give you an error? Please paste the full command with all arguments in your reply.
Also, can you also try to attach your data as a file, instead of pasting into the comment? There's likely something wrong with the format of the data file or with the command that you used?
ofleitas
commented
9 months ago Hello
I am using these two command
PS C:\Users\ofm83\Documents\Projects_python\amiga-master> python amiga.py fit --input C:\Users\ofm83\Documents\Projects_python\Kp_amiga Plate_1.txt --merge-summary -o "Fit_single" --plot --plot-derivative --save-mapping-tables --save-gp-data --sample-posterior --verbose
PS C:\Users\ofm83\Documents\Projects_python\amiga-master> python amiga.py fit --input C:\Users\ofm83\Documents\Projects_python\Kp_amiga --merge-summary -o "Fit_pool" --pool-by "Isolate" --plot --plot-derivative --save-mapping-tables --save-gp-data --sample-posterior --verbose
firasmidani
commented
9 months ago I can also run these commands too without any problems on Plate_1.txt.
Can you provide the following:
ofleitas
commented
9 months ago Hello, follow the log file. The map files I can't attach. It says that is a no supported file. log.txt
firasmidani
commented
9 months ago Ok, can you provide more detail.
In an earlier message, you shared two commands, one for fitting wells individually and another for fitting after pooling by "Isolate". Did both of those commands fail or just the latter? The log.txt that you shared only gives information on the latter?
In the log file, there is a warning about missing data points (WARNING: AMiGA detected missing data. Values are missing for some replicates at the following time-points:). In the Plate_1.txt file that you shared, I see that you have an interval of 0.5 and timepoints range from 0 to 24. Is this the same for all your files in the data folder? Do the files actually have the time listed in the first row? Did you change any of the default values in the libs/config.py file including interval in line 27 or units in lines 22 and 23?
Given what you shared so far, I still cannot reproduce your error on my side. If the above tips can't help you resolve your issue, I can still try to reproduce the error, but to do so I need all of your data and mapping files. So, I would recommend that you simply zip your work folder: "C:\Users\ofm83\Documents\Projects_python\Kp_amiga" and email it to me. My address is here.
ofleitas
commented
9 months ago Follow the log.txt of the first command. The interval of 0.5 and timepoints range from 0 to 24 are the same all the files in data folder. I changed the units to:
config['time_input_unit'] = 'hours' config['time_output_unit'] = 'hours'
And I also change the interval
config['interval'] = 0.5 # units ared based on 'time_input_unit' above
firasmidani
commented
9 months ago I looked at your mapping files. In the Plate_ID columns, make sure that the values of that column match the name of the file. All of your mapping files have only the "Plate_1" value. Fix your mapping files and re-try to run the amiga fit commnads.
ofleitas
commented
9 months ago It worked fine. Thank you very much for the help!!!
On Wed, Dec 13, 2023 at 9:49 AM Firas Midani @.***> wrote:
I looked at your mapping files. In the Plate_ID columns, make sure that the values of that column match the name of the file. All of your mapping files have only the "Plate_1" value. Fix it and confirm that it works.
— Reply to this email directly, view it on GitHub https://github.com/firasmidani/amiga/issues/20#issuecomment-1854183276, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM624NG2VA4RUTEDBE7XW7TYJHFAPAVCNFSM6AAAAABADWJ3Y2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJUGE4DGMRXGY . You are receiving this because you authored the thread.Message ID: @.***>
Hello
I am trying to do an analysis with AMIGA but I get the following error.
Traceback (most recent call last): File "amiga.py", line 400, in
AMiGA()
File "amiga.py", line 90, in init
getattr(self, args.command)()
File "amiga.py", line 346, in summarize
Command(args).summarize()
File "C:\Users\ofm83\Documents\Projects_python\amiga-master\libs\commands.py", line 71, in init
save=args.save_mapping_tables,verbose=args.verbose)
File "C:\Users\ofm83\Documents\Projects_python\amiga-master\libs\detail.py", line 108, in assembleMappings
df_mapping = initKeyFromMeta(meta_info,well_ids)
File "C:\Users\ofm83\Documents\Projects_python\amiga-master\libs\detail.py", line 323, in initKeyFromMeta
df_meta.index = well_ids
File "C:\Users\ofm83\AppData\Local\Programs\Python\Python36\lib\site-packages\pandas\core\generic.py", line 5192, in setattr
return object.setattr(self, name, value)
File "pandas/_libs/properties.pyx", line 67, in pandas._libs.properties.AxisProperty.set
File "C:\Users\ofm83\AppData\Local\Programs\Python\Python36\lib\site-packages\pandas\core\generic.py", line 690, in _set_axis
self._data.set_axis(axis, labels)
File "C:\Users\ofm83\AppData\Local\Programs\Python\Python36\lib\site-packages\pandas\core\internals\managers.py", line 183, in set_axis
"values have {new} elements".format(old=old_len, new=new_len)
ValueError: Length mismatch: Expected axis has 25 elements, new values have 5 elements