I am trying to run a github package looking at RNA-seq data for transcriptional readthrough, but seem to be running into an issue (with Pandas?).
Warning: If your Wiggle data is a significant portion of available system memory, use the --max-mem and --sort-tmpdir options, or use --do-not-sort to disable post-conversion sorting. See --help for more information.
Generating condensed genes bed...
/home/mfaleeva/.conda/envs/artdeco/lib/python3.10/site-packages/ARTDeco/preprocess.py:59: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
genes = pd.read_csv(bed_file,sep='\t',header=None,
Generating read-in region BED file...
Traceback (most recent call last):
File "/home/mfaleeva/.conda/envs/artdeco/bin/ARTDeco", line 8, in <module>
sys.exit(main())
File "/home/mfaleeva/.conda/envs/artdeco/lib/python3.10/site-packages/ARTDeco/main.py", line 423, in main
read_in_df = create_stranded_read_in_df(genes,chrom_sizes,max_len=args.intergenic_max_len,
File "/home/mfaleeva/.conda/envs/artdeco/lib/python3.10/site-packages/ARTDeco/preprocess.py", line 269, in create_stranded_read_in_df
read_in = pos_strand.append(neg_strand)
File "/home/mfaleeva/.conda/envs/artdeco/lib/python3.10/site-packages/pandas/core/generic.py", line 6296, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?
As I have not written the main body of the code, I am unsure on how to proceed. I am using the most up to date version of Pandas (2.1.1), and Python (3.10).
Any insight would be extremely appreciated!