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)
---------------------------------------------------------------------------
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
Hi, I found a new error!
ERROR
Is it possible to work on mm10 GENOME?