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lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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CRISPRessoPooledWGSCompare - hasnans #4

Closed aaiezza closed 8 years ago

aaiezza commented 8 years ago

Running the CRISPRessoPooledWGSCompare I noticed a syntax bug in the CRISPRessoPooledWGSCompareCORE.py file.

Currently the log file gives the following error:

[Command used]:
CRISPRessoPooledWGSCompare /usr/local/bin/CRISPRessoPooledWGSCompare --name A4_S186_vs_A5_S184 --sample_1_name A4_S186 --sample_2_name A5_S184 --output_folder /home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184 --save_also_png /home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186 /home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184

[Execution log]:

ERROR: 'numpy.bool_' object is not callable

The solution is described here on stackoverflow: pandas hasnan and I tested the field rather than the method and it worked giving the new following output:

[Command used]:
CRISPRessoPooledWGSCompare /usr/local/bin/CRISPRessoPooledWGSCompare --name A4_S186_vs_A5_S184 --sample_1_name A4_S186 --sample_2_name A5_S184 --output_folder /home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184 --save_also_png /home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186 /home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184

[Execution log]:
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_Fmn1" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_Fmn1" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_Fmn1" -n2 "A5_S184_Fmn1"
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_Dntt" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_Dntt" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_Dntt" -n2 "A5_S184_Dntt"
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_Ankrd10" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_Ankrd10" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_Ankrd10" -n2 "A5_S184_Ankrd10"
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_Mt1" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_Mt1" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_Mt1" -n2 "A5_S184_Mt1"
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_Psmd13" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_Psmd13" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_Psmd13" -n2 "A5_S184_Psmd13"
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_Asap1" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_Asap1" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_Asap1" -n2 "A5_S184_Asap1"
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_chr10_1" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_chr10_1" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_chr10_1" -n2 "A5_S184_chr10_1"
Skipping sample chr14 since it was not processed in one or both conditions
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_chr13" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_chr13" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_chr13" -n2 "A5_S184_chr13"
Running CRISPRessoCompare:CRISPRessoCompare "/home/aiezza/amplicon_exp/cspresso/A4_S186/CRISPRessoPooled_on_A4_S186/CRISPResso_on_chr10_2" "/home/aiezza/amplicon_exp/cspresso/A5_S184/CRISPRessoPooled_on_A5_S184/CRISPResso_on_chr10_2" -o "/home/aiezza/amplicon_exp/cspresso/A4_S186_vs_A5_S184/CRISPRessoPooledWGSCompare_on_A4_S186_vs_A5_S184" -n1 "A4_S186_chr10_2" -n2 "A5_S184_chr10_2"
All Done!

best, Alex

lucapinello commented 8 years ago

Hi Alex, thanks for catching this!

Now it is should be fixed.

Luca

aaiezza commented 8 years ago

Cool. Thanks Luca.

lucapinello commented 8 years ago

Thanks to you!

2016-08-02 11:46 GMT-04:00 Alex Aiezza notifications@github.com:

Cool. Thanks Luca.

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