6.3.3.3. gtf2bed¶
The gtf2bed script converts 1-based, closed [start, end] Gene Transfer Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted data.
For convenience, we also offer gtf2starch, which performs the extra step of creating a Starch-formatted archive.
6.3.3.3.1. Dependencies¶
The gtf2bed script requires Python, version 2.5 or greater.
This script is also dependent on input that follows the GTF 2.2 specification. A GTF-format validator is available here to ensure your input follows specification.
Tip
Conversion of data which are GTF-like, but which do not follow the specification can cause IOError and other runtime exceptions. If you run into problems, please check that your input follows the GTF specification.
6.3.3.3.2. Source¶
The gtf2bed and gtf2starch conversion scripts are part of the binary and source downloads of BEDOPS. See the Installation documentation for more details.
6.3.3.3.3. Usage¶
The gtf2bed script parses GTF from standard input and prints sorted BED to standard output. The gtf2starch script uses an extra step to parse GTF to a compressed BEDOPS Starch-formatted archive, which is also directed to standard output.
Tip
By default, all conversion scripts now output sorted BED data ready for use with BEDOPS utilities. If you do not want to sort converted output, use the --do-not-sort option. Run the script with the --help option for more details.
Tip
If you are sorting data larger than system memory, use the --max-mem option to limit sort memory usage to a reasonable fraction of available memory, e.g., --max-mem 2G or similar. See --help for more details.
6.3.3.3.4. Example¶
To demonstrate these scripts, we use a sample GTF input called foo.gtf (see the Downloads section to grab this file).
chr20 protein_coding exon 9874841 9874841 . + . gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
chr20 protein_coding CDS 9873504 9874841 . + 0 gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
chr20 protein_coding exon 9877488 9877679 . + . gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448";
We can convert it to sorted BED data in the following manner:
$ gtf2bed < foo.gtf
chr20 9874840 9874841 ZNF366 . + protein_coding exon . gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366"; zero_length_insertion "True";
chr20 9873503 9874841 ZNF366 . + protein_coding CDS 0 gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
chr20 9877487 9877679 ENSBTAG00000020601 . + protein_coding exon . gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448";
Tip
After, say, performing set or statistical operations with bedops, bedmap etc., converting data back to GTF is accomplished through an awk statement that re-orders columns and shifts the coordinate index:
$ awk '{print $1"\t"$7"\t"$8"\t"($2+1)"\t"$3"\t"$5"\t"$6"\t"$9"\t"(substr($0, index($0,$10)))}' foo_subset.bed > foo_subset.gtf
Note
Zero-length insertion elements are given an extra attribute called zero_length_insertion which lets a BED-to-GTF or other parser know that the element will require conversion back to a right-closed element [a, b], where a and b are equal.
Note
Note the conversion from 1- to 0-based coordinate indexing, in the transition from GTF to BED. BEDOPS supports operations on input with any coordinate indexing, but the coordinate change made here is believed to be convenient for most end users.
