In [1]:

    

%run ~/relmapping/annot/notebooks/annot__init__.ipynb
annot_ = 'annot_ce11'
def mp(fp, annot_=annot_): return os.path.join(annot_, 'canonical_geneset', fp)


    

    




/mnt/home3/jj374/anaconda36/lib/python3.6/site-packages/statsmodels/compat/pandas.py:56: FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead.
  from pandas.core import datetools






    




os.getcwd(): /mnt/beegfs/scratch_copy/ahringer/jj374/lab/relmapping

In [2]:

    

fp_ = 'annot_ce11/canonical_geneset/WS260_ce11.transcripts.gtf.gz'
df_ = yp.read_wbgtf(fp_, parse_attr=True, coords_adj=True)
df_.head()


    

    
Out[2]:







  

    

      

      
chrom
      
source
      
feature
      
start
      
end
      
score
      
strand
      
frame
      
exon_id
      
exon_number
      
gene_biotype
      
gene_id
      
gene_source
      
locus_id
      
protein_id
      
transcript_biotype
      
transcript_id
      
transcript_source
    
  
  

    

      
0
      
chrI
      
WormBase
      
transcript
      
3746
      
3909
      
.
      
-
      
.
      
NaN
      
NaN
      
snoRNA
      
WBGene00023193
      
WormBase
      
Y74C9A.6
      
NaN
      
snoRNA
      
Y74C9A.6
      
WormBase
    
    

      
1
      
chrI
      
WormBase
      
exon
      
3746
      
3909
      
.
      
-
      
.
      
Y74C9A.6.e1
      
1.0
      
snoRNA
      
WBGene00023193
      
WormBase
      
Y74C9A.6
      
NaN
      
snoRNA
      
Y74C9A.6
      
WormBase
    
    

      
2
      
chrI
      
WormBase
      
three_prime_utr
      
4115
      
4220
      
.
      
-
      
.
      
NaN
      
NaN
      
protein_coding
      
WBGene00022277
      
WormBase
      
homt-1
      
NaN
      
protein_coding
      
Y74C9A.3
      
WormBase
    
    

      
3
      
chrI
      
WormBase
      
exon
      
4115
      
4358
      
.
      
-
      
.
      
Y74C9A.3.e5
      
5.0
      
protein_coding
      
WBGene00022277
      
WormBase
      
homt-1
      
NaN
      
protein_coding
      
Y74C9A.3
      
WormBase
    
    

      
4
      
chrI
      
WormBase
      
transcript
      
4115
      
10230
      
.
      
-
      
.
      
NaN
      
NaN
      
protein_coding
      
WBGene00022277
      
WormBase
      
homt-1
      
NaN
      
protein_coding
      
Y74C9A.3
      
WormBase
    
  

In [3]:

    

# .bed-file for masking nuisance RNAs in ce11 tracks
l_ = ['tRNA', 'snoRNA', 'miRNA', 'snRNA', 'rRNA']
c_ = ['chrom', 'start', 'end', 'gene_id', 'score', 'strand', 'transcript_biotype']
q_ = '(feature == "transcript") & (transcript_biotype in @l_)'
fp_ = mp('WS260_ce11.transcripts.non_coding.bed')
df_.query(q_)[c_].reset_index(drop=True).to_csv(fp_, **yp.TO_GTF_KWARGS)
!wc -l {fp_}


    

    




1561 annot_ce11/canonical_geneset/WS260_ce11.transcripts.non_coding.bed