Experimental Genbank XML to GFF
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
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew gb2gff
The java jar file will be installed in the dist
directory.
20180215
The project is licensed under the MIT license.
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
$ 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 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.