How do I get data that maps the protein domain of the Interpro database to the hg19 genome coordinates?

Question

[eric.kai0918]

Hi,

How do I get data that maps the protein domain of the Interpro database to the hg19 genome coordinates? For example, I want to these format; Chromosome, StartPosition, EndPosition, ProteinDomain

Thanks.

Answer 1

[Pierre Lindenbaum]

I've written http://lindenb.github.io/jvarkit/MapUniProtFeatures.html

but I've not used it since I've written it.

$ java  -jar dist/mapuniprot.jar \
    -R /path/to/human_g1k_v37.fasta \
    -u /path/uri/uniprot.org/uniprot_sprot.xml.gz  \
    -k <(curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" | gunzip -c | awk -F '        ' '{if($2 ~ ".*_.*") next; OFS="       "; gsub(/chr/,"",$2);print;}'   ) |\
    LC_ALL=C sort -t '  ' -k1,1 -k2,2n -k3,3n  | uniq | head


1   69090   69144   topological_domain  1000    +   69090   69144   255,0,0 1   54  0
1   69144   69216   transmembrane_region    1000    +   69144   69216   255,0,0 1   72  0
1   69216   69240   topological_domain  1000    +   69216   69240   255,0,0 1   24  0
1   69240   69306   transmembrane_region    1000    +   69240   69306   255,0,0 1   66  0
1   69306   69369   topological_domain  1000    +   69306   69369   255,0,0 1   63  0
1   69357   69636   disulfide_bond  1000    +   69357   69636   255,0,0 1   279 0
1   69369   69429   transmembrane_region    1000    +   69369   69429   255,0,0 1   60  0
1   69429   69486   topological_domain  1000    +   69429   69486   255,0,0 1   57  0
1   69486   69543   transmembrane_region    1000    +   69486   69543   255,0,0 1   57  0
1   69543   69654   topological_domain  1000    +   69543   69654   255,0,0 1   111 0

[eric.kai0918]

Thank you for your answer.

[Shicheng Guo]

I notice both fasta and knowngene are based on hg19. Should I be careful about the version of uniprot_sprot.xml.gz?

I hope uniprot_sprot.xml.gz is hg19 and hg38 independent.