Reference Building

Truncate Reference GTF

xpresstools.truncate ( input_gtf, truncate_amount=45, save_coding_path=’./’, save_truncated_path=’./’, sep=’t’, return_files=False )

Purpose:

Create a GTF reference file with only protein coding genes and the first n nucleotides of each first exon

By default, will output modified GTFs to the current working directory

Assumptions:

- Input file is a properly formatted GTF file

- Protein coding transcripts are denoted by ‘protein_coding in the final column of the GTF’

Parameters:

input_gtf: GTF reference file path and name

truncate_amount: Number of nucleotides to truncate from the 5’ end of each exon 1. Considers strandedness. (default: 45). If value equals None, truncation step will not be performed and only a coding-only reference will be created

save_coding_path: Location to save coding-only GTF, set to None to avoid outputting file

save_truncated_path: Location to save coding-only truncated GTF

sep: Separator type of the GTF file (generally always tab-delimited)

return_files: If not false, will return coding only and truncated/coding only dataframes

Returns:

coding: Pandas dataframe with coding_only reference entries if return_files=True

truncated: Pandas dataframe with coding_only/truncated reference entries if return_files=True

Examples:

> import pandas as pd
> import xpresstools as xp
> gtf_coding, gtf_truncated = xp.truncate ('./transcripts.gtf', truncate_amount=45, save_coding_path=None, save_truncated_path=None, sep='\t', return_files=True)
> gtf_orig
  0 1       2           3     4     5 6 7 8
0 1 havana  gene        11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; g...
1 1 havana  transcript  11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; t...
2 1 havana  exon        11869 12227 . + . gene_id "ENSG00000223972"; exon "5"; t...
3 1 havana  exon        12613 12721 . + . gene_id "ENSG00000223972"; exon "1"; t...
4 1 havana  CDS         13221 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; t...
> gtf_truncated
  0 1       2           3     4     5 6 7 8
0 1 havana  gene        11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; g...
1 1 havana  transcript  11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; t...
2 1 havana  exon        11869 12227 . + . gene_id "ENSG00000223972"; exon "5"; t...
3 1 havana  exon        12658 12721 . + . gene_id "ENSG00000223972"; exon "1"; t...
4 1 havana  exon        13221 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; t...