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ValueError: columns cannot be a set #192

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77babyy opened this issue Apr 29, 2024 · 3 comments · May be fixed by #193
Open

ValueError: columns cannot be a set #192

77babyy opened this issue Apr 29, 2024 · 3 comments · May be fixed by #193

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@77babyy
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77babyy commented Apr 29, 2024

When I use "CITE-seq-Count-R1./ SRR13724311_S1_L001_R1_001.fastq.gz-R2 SRR13724311_S1_L001_R2_001.fastq.gz-t Cmca9_tag_list_utf8.cfa-cbf 1-cbl 16-umif 17-umil 28 -cells 10000-o OUTFOLDER "is always normal. Always normal when Looking for a whitelist, Correcting cell barcodes appear later
Looking for a whitelist
Collapsing cell barcodes
Correcting umis
Traceback (most recent call last):
File "/home/wangjiawen/miniconda3/bin/CITE-seq-Count", line 8, in
sys.exit(main())
The File "/ home/wangjiawen/miniconda3 / lib/python3.9 / site - packages/cite_seq_count / main. Py", line 603, in the main
io.write_dense(
The File "/ home/wangjiawen/miniconda3 / lib/python3.9 / site - packages/cite_seq_count/IO. Py", 48, the line in write_dense
pandas_dense = pd.DataFrame(sparse_matrix.todense(), columns=columns, index=index)
The File "/ home/wangjiawen/miniconda3 / lib/python3.9 / site - packages/pandas/core/frame. Py", line 744, in init
raise ValueError("columns cannot be a set")
ValueError: columns cannot be a set, how do I solve this problem, this seems to be a python package error
@77babyy
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77babyy commented Apr 29, 2024

Thanks a lot, I use pandas 1.4.0 to solve this problem.

@77babyy
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77babyy commented Apr 29, 2024

My output file is
"drwxr-xr-x 2 89 Apr 29 12:50 read_count
-rw-r--r-- 1 605 Apr 29 12:50 run_report.yaml
drwxr-xr-x 2 89 Apr 29 12:50 umi_count
drwxr-xr-x 2 36 Apr 29 12:50 uncorrected_cells
-rw-r--r-- 1 9711 Apr 29 12:50 unmapped.csv", the feature/barcode and matrix here are in R language, error occurs when reading 10x data“

counts <- Read10X("/pool2/wangjiawen/fastq_2/SRR13724311/OUTFOLDER/read_count/")
Error in [.data.frame(feature.names, , gene.column) :
undefined columns selected
counts <- Read10X("/pool2/wangjiawen/fastq_2/SRR13724311/OUTFOLDER/umi_count/")
Error in [.data.frame(feature.names, , gene.column) :
undefined columns selected”, what should I do？

@lemon-latte
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import data into R by following code:
counts <- Read10X("/pool2/wangjiawen/fastq_2/SRR13724311/OUTFOLDER/umi_count/",gene.column = 1)

My output file is "drwxr-xr-x 2 89 Apr 29 12:50 read_count -rw-r--r-- 1 605 Apr 29 12:50 run_report.yaml drwxr-xr-x 2 89 Apr 29 12:50 umi_count drwxr-xr-x 2 36 Apr 29 12:50 uncorrected_cells -rw-r--r-- 1 9711 Apr 29 12:50 unmapped.csv", the feature/barcode and matrix here are in R language, error occurs when reading 10x data“

counts <- Read10X("/pool2/wangjiawen/fastq_2/SRR13724311/OUTFOLDER/read_count/")
Error in [.data.frame(feature.names, , gene.column) :
undefined columns selected
counts <- Read10X("/pool2/wangjiawen/fastq_2/SRR13724311/OUTFOLDER/umi_count/")
Error in [.data.frame(feature.names, , gene.column) :
undefined columns selected”, what should I do？

dtenenba added a commit to dtenenba/CITE-seq-Count that referenced this issue Jul 22, 2024
@dtenenba
Convert columns from set to list before creating pd.DataFrame()
22e9c44 
Closes Hoohm#192 

Pandas' DataFrame() constructor used to accept a `set` as its `columns` argument, but no longer does.

This simply converts the `set` to a `list` before creating the data frame.
There may be better approaches to deal with this issue, but I'm not familiar enough with this package to know about them.
@dtenenba dtenenba linked a pull request Jul 22, 2024 that will close this issue
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Convert columns from set to list before creating pd.DataFrame() dtenenba/CITE-seq-Count
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@lemon-latte @77babyy