genome error

[feanaros]

Hi, I found a new error!

from LingerGRN.preprocess import *
Datadir='/home/baldini/sc/tbx1-2022/python_analysis/LINGER/'# This directory should be the same as Datadir defined in the above 'Download the general gene regulatory network' section
GRNdir=Datadir+'data_bulk/'
genome='mm10'
outdir='/home/baldini/sc/tbx1-2022/python_analysis/LINGER/output' #output dir
preprocess(TG_pseudobulk,RE_pseudobulk,GRNdir,genome,method,outdir)

ERROR

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[14], line 6
      4 genome='mm10'
      5 outdir='/home/baldini/sc/tbx1-2022/python_analysis/LINGER/output' #output dir
----> 6 preprocess(TG_pseudobulk,RE_pseudobulk,GRNdir,genome,method,outdir)

File ~/anaconda3/envs/LINGER/lib/python3.10/site-packages/LingerGRN/preprocess.py:214, in preprocess(TG_pseudobulk, RE_pseudobulk, GRNdir, genome, method, outdir)
    206 def preprocess(TG_pseudobulk,RE_pseudobulk,GRNdir,genome,method,outdir):
    207     #package_dir = os.path.dirname(os.path.abspath(__file__))
    208     if method=='LINGER':
    209         #print('Overlap the regions with bulk data ...')
    210         #script_path = os.path.join("extract_overlap_regions_LINGER.sh")
    211         #subprocess.run(["sh", script_path, GRNdir, genome,outdir,workdir])
    212         #print('Generate pseudobulk ...')
    213         #TG_pseudobulk,RE_pseudobulk=pseudo_bulk.pseudo_bulk(adata_RNA,adata_ATAC)
--> 214         extract_overlap_regions(genome,GRNdir,outdir,method)
    215         print('Mapping gene expression...')
    216         TFName = pd.read_csv(GRNdir+'TFName.txt',header=None)

File ~/anaconda3/envs/LINGER/lib/python3.10/site-packages/LingerGRN/preprocess.py:166, in extract_overlap_regions(genome, GRNdir, outdir, method)
    164     a_with_b=pd.read_csv(outdir+'temp.bed',sep='\t',header=None)
    165     a_with_b[[6,7,8,0,1,2]].to_csv(outdir+'match_hg19_peak.bed',sep='\t',header=None,index=None)
--> 166 a = pybedtools.example_bedtool(outdir+'match_hg19_peak.bed')
    167 b = pybedtools.example_bedtool(GRNdir+'RE_gene_corr_hg19.bed')
    168 a_with_b = a.intersect(b, wa=True,wb=True)

File ~/anaconda3/envs/LINGER/lib/python3.10/site-packages/pybedtools/bedtool.py:3915, in example_bedtool(fn)
   3913 if not os.path.exists(fn):
   3914     msg = "%s does not exist" % fn
-> 3915     raise FileNotFoundError(msg)
   3916 return BedTool(fn)

FileNotFoundError: /home/baldini/sc/tbx1-2022/python_analysis/LINGER/outputmatch_hg19_peak.bed does not exist

Is it possible to work on mm10 GENOME?

[amssyqy]

Thanks for using LINGER! We are still working on mm10 and other species~ Thanks for your time~

[feanaros]

i Hope soon 🥺