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Hoohm / CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay
https://hoohm.github.io/CITE-seq-Count/
MIT License
79 stars 44 forks source link

ValueError: columns cannot be a set #192

Open 77babyy opened 6 months ago

77babyy commented 6 months ago

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 commented 6 months ago

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

77babyy commented 6 months ago

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 commented 5 months ago

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？