my proposed changes

[lldelisle]

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

[Hoohm]

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.

In .travis.yml https://github.com/Hoohm/CITE-seq-Count/pull/185#discussion_r1402715936:

@@ -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...

— Reply to this email directly, view it on GitHub https://github.com/Hoohm/CITE-seq-Count/pull/185#discussion_r1402715936, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJVO2F2VZUNKPJSE2MRQUTYFZTGJAVCNFSM6AAAAAA7WQQ63GVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTONBVGM4DGOJWGQ . You are receiving this because you commented.Message ID: @.***>