Linux based enzyme restriction tool

[papori]

Hi all,
I guess that the answer should be simple, but honestly i googled it and didnt find the answe...
What im looking for is linux based tool to recognize enzyme restriction sites:
1) over the genome (reference genome)
2) over SAM/BAM file

Right now what im doing is simply using Bowtie2 for multiple perfect hits to solve the first problem (reference genome), but it cant solve the SAM/BAM file.
Moreover, i want to go over all the the rebase database (http://rebase.neb.com/rebase/rebase.ftp.html), and im sure there is already a tool that doing it...

Any ideas?
Thanks,
Pap

[lindenb]

I wrote a genomic digester , see https://www.biostars.org/p/86480/#86535

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr3.fa.gz" |\
gunzip -c  |\
java -jar dist/biostar86480.jar -E AarI -E EcoRI 

chr3    60645    60651    GAATTC    1000    +    EcoRI    G^AATTC
chr3    60953    60959    GAATTC    1000    +    EcoRI    G^AATTC
chr3    68165    68172    GCAGGTG    1000    -    AarI    CACCTGC(4/8)
chr3    70263    70269    GAATTC    1000    +    EcoRI    G^AATTC
chr3    70945    70952    GCAGGTG    1000    -    AarI    CACCTGC(4/8)
chr3    71140    71146    GAATTC    1000    +    EcoRI    G^AATTC
chr3    72264    72270    GAATTC    1000    +    EcoRI    G^AATTC
chr3    74150    74156    GAATTC    1000    +    EcoRI    G^AATTC
chr3    75063    75069    GAATTC    1000    +    EcoRI    G^AATTC
chr3    78438    78444    GAATTC    1000    +    EcoRI    G^AATTC
chr3    81052    81059    CACCTGC    1000    +    AarI    CACCTGC(4/8)
chr3    84498    84504    GAATTC    1000    +    EcoRI    G^AATTC
chr3    84546    84552    GAATTC    1000    +    EcoRI    G^AATTC
chr3    84780    84787    CACCTGC    1000    +    AarI    CACCTGC(4/8)
chr3    87771    87777    GAATTC    1000    +    EcoRI    G^AATTC
chr3    95344    95351    GCAGGTG    1000    -    AarI    CACCTGC(4/8)
chr3    96358    96364    GAATTC    1000    +    EcoRI    G^AATTC
chr3    96734    96740    GAATTC    1000    +    EcoRI    G^AATTC
chr3    105956    105962    GAATTC    1000    +    EcoRI    G^AATTC

[papori]

Thanks lindenb!
I saw your post before,but i have there a compliation error and our system admin is not in the area.. so we cant install anything right now..
The error is about the "Requires apache ANT."

Anyway, can it solve also the SAM/BAM problem?

Thanks,
Pap

I wrote a genomic digester , see https://www.biostars.org/p/86480/#86535

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr3.fa.gz" |\
gunzip -c  |\
java -jar dist/biostar86480.jar -E AarI -E EcoRI 

chr3    60645    60651    GAATTC    1000    +    EcoRI    G^AATTC
chr3    60953    60959    GAATTC    1000    +    EcoRI    G^AATTC
chr3    68165    68172    GCAGGTG    1000    -    AarI    CACCTGC(4/8)
chr3    70263    70269    GAATTC    1000    +    EcoRI    G^AATTC
chr3    70945    70952    GCAGGTG    1000    -    AarI    CACCTGC(4/8)
chr3    71140    71146    GAATTC    1000    +    EcoRI    G^AATTC
chr3    72264    72270    GAATTC    1000    +    EcoRI    G^AATTC
chr3    74150    74156    GAATTC    1000    +    EcoRI    G^AATTC
chr3    75063    75069    GAATTC    1000    +    EcoRI    G^AATTC
chr3    78438    78444    GAATTC    1000    +    EcoRI    G^AATTC
chr3    81052    81059    CACCTGC    1000    +    AarI    CACCTGC(4/8)
chr3    84498    84504    GAATTC    1000    +    EcoRI    G^AATTC
chr3    84546    84552    GAATTC    1000    +    EcoRI    G^AATTC
chr3    84780    84787    CACCTGC    1000    +    AarI    CACCTGC(4/8)
chr3    87771    87777    GAATTC    1000    +    EcoRI    G^AATTC
chr3    95344    95351    GCAGGTG    1000    -    AarI    CACCTGC(4/8)
chr3    96358    96364    GAATTC    1000    +    EcoRI    G^AATTC
chr3    96734    96740    GAATTC    1000    +    EcoRI    G^AATTC
chr3    105956    105962    GAATTC    1000    +    EcoRI    G^AATTC

[lindenb]

I don't think you need a sysadmin ,just download ant from http://ant.apache.org/bindownload.cgi and add the executable to your PATH.

Running this for a SAM file would be easy but I just wonder why you would need this ... :-)