jvarkit

GenbankToGff3

Experimental Genbank XML to GFF

Usage

Usage: gb2gff [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• xml
• ncbi
• genbank
• convert
• gff
• gb

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew gb2gff

The java jar file will be installed in the dist directory.

Creation Date

20180215

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/genbank/GenbankToGff3.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite gb2gff ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Warnings

• still experimental
• efetch doesn’t always work: https://gist.github.com/lindenb/6c4f36bdf29a3108e103e3a5a0b1aff7

Example

$ wget -O - -q  "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=AF338247.1,D38149.1&rettype=gbwithparts&retmode=xml&api_key=62b713e0cd85e6ac79699ecdfa72e85af009"  | java -jar dist/gb2gff.jar 

##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10970
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10941
##sequence-region AF338247.1 1 2032
##sequence-region D38149.1 1 1087
AF338247.1	genbank	source	1	2032	.	+	.	strain=M;db_xref=taxon:10941;note="rearranged segment 7";organism="Human rotavirus A";segment=7R;clone=M1;mol_type="genomic RNA"
AF338247.1	genbank	five_prime_UTR	1	34	.	+	.	.
AF338247.1	genbank	CDS	35	967	.	+	1	codon_start=1;product=NSP3;protein_id=AAK74117.1;transl_table=1
AF338247.1	genbank	CDS	993	1925	.	+	1	note="duplicated ORF";codon_start=1;product=NSP3;protein_id=AAK74118.1;transl_table=1
AF338247.1	genbank	three_prime_UTR	1926	2032	.	+	.	.
D38149.1	genbank	source	1	1087	.	+	.	strain=A5-16;db_xref=taxon:10970;organism="Rotavirus sp.";segment=5;mol_type="genomic RNA"
D38149.1	genbank	gene	33	185	.	+	.	gene=NSP1
D38149.1	genbank	CDS	33	185	.	+	1	codon_start=1;protein_id=BAA07347.1;gene=NSP1;transl_table=1
D38149.1	genbank	variation	141	141	.	+	.	note="bases 142-641 in D38148 deleted";gene=NSP1

input

Input is a list of *.xml genbank files (DTD/Schema: https://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd ). Otherwise assume that file is a list of filenames and unfold it.

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