ATG

Convert your genomic reference data between formats with a single tool. ATG handles the conversion from and to GTF, GenePred(ext) and Refgene. You can generate bed files, fasta sequences or custom feature sequences. A single tool for all your conversion.

File format	Can be used as source	Can be created
GTF	Yes	Yes
GenePred (extended)	Yes	Yes
RefGene	Yes	Yes
GenePred (simple)	No	Yes
Bed	No	Yes
Fasta	No	Yes (multiple options)

Reasons to use ATG

No need to maintain multiple tools for one-way conversions (gtfToGenePred, genePredToGtf, etc). ATG handles many formats and can convert in both directions.
Speed: ATG is really fast - almost twice as fast as gtfToGenePred.
Robust parser: It handles GTF, GenePred with all extras according to spec.
Low memory footprint: It also runs on machines with little RAM.
Open for contributions: Every help is welcome improve ATG or to add more functionality.
You can also use ATG as a library for your own Rust projects.

ATG command line tool

Install

There are currently 3 different options how to install ATG:

cargo

The easiest way to install ATG is to use cargo (if you have cargo and rust installed)

cargo install atg

Pre-built binaries

You can download pre-built binaries for Linux and Mac (M1) from Github.

From source

You can also build ATG from source (if you have the rust toolchains installed):

git clone https://github.com/anergictcell/atg.git
cd atg
cargo build --release

Usage

The main CLI arguments are

-f, --from: Specify the file format of the source (e.g. gtf, genepredext, refgene)
-t, --to: Specify the target file format (e.g. gtf, genepred, bed, fasta etc)
-i, --input: Path to source file. (Use /dev/stdin if you are using atg in a pipe)
-o, --output: Path to target file. Existing files will be overwritten. (Use /dev/stdout if you are using atg in a pipe)
-v, -vv, -vvv: Verbosity (info, debug, trace)
-h, --help: Print the help dialog with detailed usage instructions.

Additional, optional arguments:

-g, --gtf-source: Specify the source for GTF output files. Defaults to atg
-r, --reference: Path of a reference genome fasta file. Required for fasta output

Examples:

## Convert a GTF file to a RefGene file
atg --from gtf --to refgene --input /path/to/input.gtf --output /path/to/output.refgene

## Convert a GTF file to a GenePred file
atg --from gtf --to genepred --input /path/to/input.gtf --output /path/to/output.genepred

## Convert a GTF file to a GenePredExt file
atg --from gtf --to genepredext --input /path/to/input.gtf --output /path/to/output.genepredext

## Convert RefGene to GTF
atg --from refgene --to gtf --input /path/to/input.refgene --output /path/to/output.gtf

## Convert RefGene to bed
atg --from refgene --to bed --input /path/to/input.refgene --output /path/to/output.bed

Supported `--output` formats

gtf

Output in GTF format.

chr9    ncbiRefSeq.2021-05-17   transcript  74526555    74600974    .   +   .   gene_id "C9orf85"; transcript_id "NM_001365057.2";
chr9    ncbiRefSeq.2021-05-17   exon        74526555    74526752    .   +   .   gene_id "C9orf85"; transcript_id "NM_001365057.2";
chr9    ncbiRefSeq.2021-05-17   5UTR        74526555    74526650    .   +   .   gene_id "C9orf85"; transcript_id "NM_001365057.2";
chr9    ncbiRefSeq.2021-05-17   CDS         74526651    74526752    .   +   0   gene_id "C9orf85"; transcript_id "NM_001365057.2";
chr9    ncbiRefSeq.2021-05-17   exon        74561922    74562028    .   +   .   gene_id "C9orf85"; transcript_id "NM_001365057.2";
chr9    ncbiRefSeq.2021-05-17   CDS         74561922    74562026    .   +   0   gene_id "C9orf85"; transcript_id "NM_001365057.2";
...

You can specify the value of the source column manually using the --gtf-source/-g option. Defaults to atg

refgene

Output in the refGene format, as used by some UCSC and NCBI RefSeq services

0   NM_001101.5     chr7    -   5566778     5570232     5567378     5569288    6   5566778,5567634,5567911,5568791,5569165,5570154,    5567522,5567816,5568350,5569031,5569294,5570232,    0   ACTB    cmpl    cmpl    0,1,0,0,0,-1,
0   NM_001203247.2  chr7    -   148504474   148581383   148504737   148544390  20  148504474,148506162,148506401,148507424,148508716,148511050,148512005,148512597,148513775,148514313,148514968,148516687,148523560,148524255,148525831,148526819,148529725,148543561,148544273,148581255,    148504798,148506247,148506482,148507506,148508812,148511229,148512131,148512638,148513870,148514483,148515209,148516779,148523724,148524358,148525972,148526940,148529842,148543690,148544397,148581383,    0   EZH2    cmpl    cmpl    2,1,1,0,0,1,1,2,0,1,0,1,2,1,1,0,0,0,0,-1,
0   NM_001203248.2  chr7    -   148504474   148581383   148504737   148544390  20  148504474,148506162,148506401,148507424,148508716,148511050,148512005,148512597,148513775,148514313,148514968,148516687,148523560,148524255,148525831,148526819,148529725,148543588,148544273,148581255,    148504798,148506247,148506482,148507506,148508812,148511229,148512131,148512638,148513870,148514483,148515209,148516779,148523724,148524358,148525972,148526940,148529842,148543690,148544397,148581383,    0   EZH2    cmpl    cmpl    2,1,1,0,0,1,1,2,0,1,0,1,2,1,1,0,0,0,0,-1,
0   NM_001354750.2  chr11   +   113930432   114127487   113934022   114121277  7   113930432,113933932,114027058,114057673,114112888,114117919,114121047,  113930864,113935290,114027156,114057760,114113059,114118087,114127487,  0   ZBTB16  cmpl    cmpl    -1,0,2,1,1,1,1,

genepred(ext)

Output in the GenePred(Ext) format, as used by some UCSC and NCBI RefSeq services

GenePred:

NM_001101.5     chr7    -   5566778     5570232     5567378     5569288     6   5566778,5567634,5567911,5568791,5569165,5570154,    5567522,5567816,5568350,5569031,5569294,5570232,
NM_001203247.2  chr7    -   148504474   148581383   148504737   148544390   20  148504474,148506162,148506401,148507424,148508716,148511050,148512005,148512597,148513775,148514313,148514968,148516687,148523560,148524255,148525831,148526819,148529725,148543561,148544273,148581255,    148504798,148506247,148506482,148507506,148508812,148511229,148512131,148512638,148513870,148514483,148515209,148516779,148523724,148524358,148525972,148526940,148529842,148543690,148544397,148581383,
NM_001203248.2  chr7    -   148504474   148581383   148504737   148544390   20  148504474,148506162,148506401,148507424,148508716,148511050,148512005,148512597,148513775,148514313,148514968,148516687,148523560,148524255,148525831,148526819,148529725,148543588,148544273,148581255,    148504798,148506247,148506482,148507506,148508812,148511229,148512131,148512638,148513870,148514483,148515209,148516779,148523724,148524358,148525972,148526940,148529842,148543690,148544397,148581383,
NM_001354750.2  chr11   +   113930432   114127487   113934022   114121277   7   113930432,113933932,114027058,114057673,114112888,114117919,114121047,  113930864,113935290,114027156,114057760,114113059,114118087,114127487,

GenePredExt

NM_001101.5     chr7    -   5566778     5570232     5567378     5569288     6   5566778,5567634,5567911,5568791,5569165,5570154,    5567522,5567816,5568350,5569031,5569294,5570232,    0   ACTB    cmpl    cmpl    0,1,0,0,0,-1,
NM_001203247.2  chr7    -   148504474   148581383   148504737   148544390   20  148504474,148506162,148506401,148507424,148508716,148511050,148512005,148512597,148513775,148514313,148514968,148516687,148523560,148524255,148525831,148526819,148529725,148543561,148544273,148581255,    148504798,148506247,148506482,148507506,148508812,148511229,148512131,148512638,148513870,148514483,148515209,148516779,148523724,148524358,148525972,148526940,148529842,148543690,148544397,148581383,    0   EZH2    cmpl    cmpl    2,1,1,0,0,1,1,2,0,1,0,1,2,1,1,0,0,0,0,-1,
NM_001203248.2  chr7    -   148504474   148581383   148504737   148544390   20  148504474,148506162,148506401,148507424,148508716,148511050,148512005,148512597,148513775,148514313,148514968,148516687,148523560,148524255,148525831,148526819,148529725,148543588,148544273,148581255,    148504798,148506247,148506482,148507506,148508812,148511229,148512131,148512638,148513870,148514483,148515209,148516779,148523724,148524358,148525972,148526940,148529842,148543690,148544397,148581383,    0   EZH2    cmpl    cmpl    2,1,1,0,0,1,1,2,0,1,0,1,2,1,1,0,0,0,0,-1,
NM_001354750.2  chr11   +   113930432   114127487   113934022   114121277   7   113930432,113933932,114027058,114057673,114112888,114117919,114121047,  113930864,113935290,114027156,114057760,114113059,114118087,114127487,  0   ZBTB16  cmpl    cmpl    -1,0,2,1,1,1,1,

bed

Output in bed format.

chr7    5566778     5570232     ACTB:NM_001101.5       -   5567378    5569288    212,16,48   6   744,182,439,240,129,78  0,856,1133,2013,2387,3376
chr11   113930432   114127487   ZBTB16:NM_001354750.2  +   113934022  114121277  212,16,48   7   432,1358,98,87,171,168,6440 0,3500,96626,127241,182456,187487,190615
chr17   40852292    40897058    EZH1:NM_001321082.2    -   40854549   40880959   212,16,48   20  2318,85,81,82,96,179,126,41,92,197,181,92,164,103,177,121,129,128,91,30 0,2602,3465,4327,4813,5732,7683,8601,9571,12014,12934,17701,18179,18830,19998,22520,27360,28550,30553,44736

fasta

Writes the cDNA sequence of all transcripts into one file. Please note that the sequence is stranded.

This target format requires a reference genome fasta file that must be specified using --reference/-r.

This output allows different --fasta-format options:

transcript: The full transcript sequence (from the genomic start to end position, including introns)
exons: The cDNA sequence of the processed transcript, i.e. the sequence of all exons, including non-coding exons.
cds (default): The CDS of the transcript

>NM_007298.3 BRCA1
ATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGC
TATGCAGAAAATCTTAGAGTGTCCCATCTGTCTGGAGTTGATCAAGGAAC
CTGTCTCCACAAAGTGTGACCACATATTTTGCAAATTTTGCATGCTGAAA
CTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGA
TATAACCAAAAGGAGCCTACAAGAAAGTACGAGATTTAGTCAACTTGTTG
...
>NM_001365057.2 C9orf85
ATGAGCTCCCAGAAAGGCAACGTGGCTCGTTCCAGACCTCAGAAGCACCA
GAATACGTTTAGCTTCAAAAATGACAAGTTCGATAAAAGTGTGCAGACCA
AGAAAATTAATGCAAAACTTCATGATGGAGTATGTCAGCGCTGTAAAGAA
GTTCTTGAGTGGCGTGTAAAATACAGCAAATACAAACCATTATCAAAACC
TAAAAAGTGA
...

fasta-split

Like fasta above, but one file for each transcript. Instead of an output file, you must specify an output directory, ATG will save each transcript as <Transcript_name>.fasta, e.g.: NM_001365057.2.fasta.

This target format requires a reference genome fasta file that must be specified using --reference/-r.

This output allows different --fasta-format options:

transcript: The full transcript sequence (from the genomic start to end position, including introns)
exons: The cDNA sequence of the processed transcript, i.e. the sequence of all exons, including non-coding exons.
cds (default): The CDS of the transcript

feature-sequence

cDNA sequence of each feature (5' UTR, CDS, 3'UTR), each in a separate row.

This target format requires a reference genome fasta file that must be specified using --reference/-r.

BRCA1   NM_007298.3     chr17   41196311    41197694    -   3UTR    CTGCAGCCAGCCAC...
BRCA1   NM_007298.3     chr17   41197694    41197819    -   CDS     CAATTGGGCAGATGTGTG...
BRCA1   NM_007298.3     chr17   41199659    41199720    -   CDS     GGTGTCCACCCAATTGTG...
BRCA1   NM_007298.3     chr17   41201137    41201211    -   CDS     ATCAACTGGAATGGATGG...
BRCA1   NM_007298.3     chr17   41203079    41203134    -   CDS     ATCTTCAGGGGGCTAGAA...
BRCA1   NM_007298.3     chr17   41209068    41209152    -   CDS     CATGATTTTGAAGTCAGA...
BRCA1   NM_007298.3     chr17   41215349    41215390    -   CDS     GGGTGACCCAGTCTATTA...
BRCA1   NM_007298.3     chr17   41215890    41215968    -   CDS     ATGCTGAGTTTGTGTGTG...
BRCA1   NM_007298.3     chr17   41219624    41219712    -   CDS     ATGCTCGTGTACAAGTTT...
BRCA1   NM_007298.3     chr17   41222944    41223255    -   CDS     AGGGAACCCCTTACCTGG...
C9orf85 NM_001365057.2  chr9    74526555    74526650    +   5UTR    ATTGACAGAA...
C9orf85 NM_001365057.2  chr9    74526651    74526752    +   CDS     ATGAGCTCCCAGAA...
C9orf85 NM_001365057.2  chr9    74561922    74562028    +   CDS     AAAATTAATGCAAA...
C9orf85 NM_001365057.2  chr9    74597573    74597573    +   CDS     A
C9orf85 NM_001365057.2  chr9    74597574    74600974    +   3UTR    TGGAGTCTCC...

raw

This is mainly useful for debugging, as it gives a quick glimpse into the Exons and CDS coordinates of the transcripts.

bin

Save Transcripts in ATG binary format for faster re-reading.

Tips

ATG as library

The library API is mostly documented inline and available on docs.rs

Examples

Convert GTF to RefGene

use atg::gtf::Reader;
use atg::refgene::Writer;
use atg::models::{TranscriptRead, TranscriptWrite};

let mut reader = Reader::from_file("tests/data/example.gtf")
    .unwrap_or_else(|_| panic!("Error opening input file."));

let mut writer = Writer::from_file("/dev/null")
    .unwrap_or_else(|_| panic!("Unable to open output file"));

let transcripts = reader.transcripts()
    .unwrap_or_else(|err| panic!("Error parsing GTF: {}", err));

match writer.write_transcripts(&transcripts) {
    Ok(_) => println!("Success"),
    Err(err) => panic!("Error writing RefGene file: {}", err)
};

ToDo / Next tasks

Add to crates.io
Bed module to generate bed files with exons and introns
GenePred & GenePredExt modules
Compare transcripts from two different inputs
Add fasta reading for nt and aa sequence outputs
Binary data format
use Smartstring or Smallstr for gene-symbol, transcript name and chromosome
Remove function to sanitize chromosome name with chr prefix
Parallelize input parsing
Check if exons can be stored in smaller vec
Use std::mem::replace to move out of attributes, e.g. in TranscriptBuilder and remove Copy/Clone traits https://stackoverflow.com/questions/31307680/how-to-move-one-field-out-of-a-struct-that-implements-drop-trait

Known issues

GTF parsing

NM_001371720.1 has two book-ended exons (155160639-155161619 || 155161620-155162101). During input parsing, book-ended features are merged into one exon

atg 0.5.0

ATG

ATG command line tool

Install

cargo

Pre-built binaries

From source

Usage

Examples:

Supported --output formats

gtf

refgene

genepred(ext)

bed

fasta

fasta-split

feature-sequence

raw

bin

Tips

ATG as library

Examples

Convert GTF to RefGene

ToDo / Next tasks

Known issues

GTF parsing

Supported `--output` formats