my proposed changes #185
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my proposed changes #185
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lldelisle
commented
Nov 22, 2023
| @@ -19,11 +19,10 @@ install: | |||
| - conda config --add channels defaults | |||
| - conda config --add channels conda-forge | |||
| - conda config --add channels bioconda | |||
| - conda install -c bioconda -c conda-forge snakemake | |||
| - conda create -q -n snakemake snakemake>=5.3.1 python=3.6 | |||
| - conda create -q -n snakemake 'snakemake>=5.3.1' 'python>=3.10' | |||
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Requires python >= 3.10 to get the | None working.
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I believe this is only for documentation updates, not the code itself.
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Aaah. But then, which python is used? It was written python3.6 setup.py install...
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I updated it on the branch to 3.11
| @@ -57,7 +57,7 @@ def parse_barcode_reference( | |||
| barcode_pattern = rf"^[ATGC]{{{barcode_length}}}" | |||
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| header = barcodes_pl.columns | |||
| set_dif = set(required_header) - set(header) | |||
| set_dif = set([required_header]) - set(header) | |||
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without the brackets it was splitting every letter of the required_header
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Keep that one in, I'll merge once the PR is ready
| @@ -74,7 +74,7 @@ def parse_barcode_reference( | |||
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| else: | |||
| barcodes_pl = barcodes_pl.with_columns( | |||
| reference=pl.col(REFERENCE_COLUMN).str.strip_chars(STRIP_CHARS), | |||
| reference=pl.col(required_header).str.strip_chars(STRIP_CHARS), | |||
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in barcodes_pl there is not the 'reference' column (at least in the whitelist barcode)
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I'm changing the behavior here a little bit. I think I'm gonna use "reference" even in the whitelist input. Just makes the logic a bit cleaner
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To test I was doing: $ python cite_seq_count/__main__.py -R1 tests/test_data/fastq/correct_R1_with_cell_barcode_mm.fastq.gz -R2 tests/test_data/fastq/correct_R2.fastq.gz -t tests/test_data/tags/pass/correct_3.csv -cbf 1 -cbl 16 -umif 17 -umil 26 -wl tests/test_data/whitelist.csv
Counting number of reads in file tests/test_data/fastq/correct_R1_with_cell_barcode_mm.fastq.gz
Writing chunks to disk
Reading reads from files: tests/test_data/fastq/correct_R1_with_cell_barcode_mm.fastq.gz, tests/test_data/fastq/correct_R2.fastq.gz
Mapping reads
Mapping done
Correcting barcodes
Barcodes corrected
Traceback (most recent call last):
File "/home/ldelisle/Documents/mygit/CITE-seq-Count/cite_seq_count/__main__.py", line 208, in <module>
main()
File "/home/ldelisle/Documents/mygit/CITE-seq-Count/cite_seq_count/__main__.py", line 101, in main
final_results=final_results,
UnboundLocalError: local variable 'final_results' referenced before assignment |
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3.11 ATM, haven't updated the setup file.
…Sent from my phone
On Wed, Nov 22, 2023, 22:13 Lucille Delisle ***@***.***> wrote:
***@***.**** commented on this pull request.
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In .travis.yml
<#185 (comment)>:
> @@ -19,11 +19,10 @@ install:
- conda config --add channels defaults
- conda config --add channels conda-forge
- conda config --add channels bioconda
- - conda install -c bioconda -c conda-forge snakemake
- - conda create -q -n snakemake snakemake>=5.3.1 python=3.6
+ - conda create -q -n snakemake 'snakemake>=5.3.1' 'python>=3.10'
Aaah. But then, which python is used? It was written python3.6 setup.py
install...
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