search

GangCaoLab / CoolBox

Jupyter notebook based genomic data visualization toolkit.
https://gangcaolab.github.io/CoolBox/index.html
GNU General Public License v3.0
224 stars 37 forks source link

bed9 detected as a bed6 #53

Open alexlenail opened 3 years ago

alexlenail commented 3 years ago

First row has 9 columns:

AssertionError: File type detected is bed6 but line 1: chr9 4679558 4703208 ENSG00000106993.11  .   +   HAVANA  transcript  .   gene_id "ENSG00000106993.11"; transcript_id "ENST00000381858.5"; gene_type "protein_coding"; gene_name "CDC37L1"; transcript_type "protein_coding"; transcript_name "CDC37L1-202"; level 2; protein_id "ENSP00000371282.1"; transcript_support_level "5"; tag "not_organism_supported"; tag "basic"; havana_gene "OTTHUMG00000019465.1"; havana_transcript "OTTHUMT00000051565.1";
 does not have 6 fields.
perinom commented 2 years ago

Same here but with bed12

Nanguage commented 2 years ago

First row has 9 columns:

AssertionError: File type detected is bed6 but line 1: chr9   4679558 4703208 ENSG00000106993.11  .   +   HAVANA  transcript  .   gene_id "ENSG00000106993.11"; transcript_id "ENST00000381858.5"; gene_type "protein_coding"; gene_name "CDC37L1"; transcript_type "protein_coding"; transcript_name "CDC37L1-202"; level 2; protein_id "ENSP00000371282.1"; transcript_support_level "5"; tag "not_organism_supported"; tag "basic"; havana_gene "OTTHUMG00000019465.1"; havana_transcript "OTTHUMT00000051565.1";
 does not have 6 fields.

seems large than 9 columns

1   2   3   4           5   6   7   8       9       10
chr9    4679558 4703208 ENSG00000106993.11  .   +   HAVANA  transcript  .   gene_id "ENSG00000106993.11"; transcript_id "ENST00000381858.5"; gene_type "protein_coding"; gene_name "CDC37L1"; transcript_type "protein_coding"; transcript_name "CDC37L1-202"; level 2; protein_id "ENSP00000371282.1"; transcript_support_level "5"; tag "not_organism_supported"; tag "basic"; havana_gene "OTTHUMG00000019465.1"; havana_transcript "OTTHUMT00000051565.1";