Xu-Dong/Exon_Intron_Extractor

1. exon and intron extractor

Description

This script parse a gtf file and extract all exons and introns for each transcript in it.

Usage:

usage: extractExon_and_Intron_from_gtf.py [-h] [--gtf GTF]
                                          [--out_exon OUT_EXON]
                                          [--out_intron OUT_INTRON]
                                          [--geneRange]

optional arguments:
  -h, --help            show this help message and exit
  --gtf GTF             specify a gtf file
  --out_exon OUT_EXON   specify a filename for exon output
  --out_intron OUT_INTRON
                        specify a filename for intron output
  --geneRange           if True (default), output gene range into a bed file:
                        geneRange.bed

output format

Two bed files containing exons and introns separately will be produced, and if "--geneRange True" (by default), a geneRange.bed file containing gene ranges will also be produced.

Both exon and intron bed files contains 8 columns, the 1 to 6 columns are standard bed file columns, the additional two columns are gene_name and gene_type, respectively. The geneRange.bed is standard bed file (6 columns).

2. gtf to bed

Description

This script convert a gtf file into a bed (bed12) file. Each row in the output bed file represents a transcript, and the blocks are exons. Currently, only transcripts in protein_coding genes and lncRNAs from autosomal and two sexual chromosomes are included.

Usage:

usage: gtf2bed12.py [-h] -g GTF [-o OUT_BED]

optional arguments:
  -h, --help            show this help message and exit
  -g GTF, --gtf GTF     specify a gtf file
  -o OUT_BED, --out_bed OUT_BED
                        specify a filename for output

output and format

1. one bed file with 12 columns will be produced. The description of bed12 format can be found in UCSC website.
2. one tab-separated file namely "transcript_to_geneName.txt" will also be produced.