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brentp / first.ucsc.bed.sh
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get the first intron and the first coding exon from UCSC database.

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first.ucsc.bed.sh
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ORG=hg19
mysql -A -D $ORG -e "SELECT chrom, txStart, txEnd, cdsStart, cdsEnd, name2, name, \
           strand, exonStarts, exonEnds from refGene;" \
           | awk 'BEGIN {FS=OFS="\t"}
            (NR>1){
                delete cstarts; delete cends;
                split($9, cstarts, ",");
                split($10, cends, ",");
                strand=$8;
                name=$6"::"$7
                if(strand == "+"){
                    # 1 based indexing...
                    print $1,cends[1],cstarts[2],name,strand
                }
                else if(strand == "-"){
                    n = length(cends) - 1 # account for trailing coma
                    print $1,cends[n-1],cstarts[n],name,strand
                }
            }' > first.introns.bed
 
 
mysql -A -D $ORG -e "SELECT chrom, txStart, txEnd, cdsStart, cdsEnd, name2, name, \
           strand, exonStarts, exonEnds from refGene;" \
           | awk 'BEGIN {FS=OFS="\t"}
            (NR>1){
                if($4==$5){ next; } # noncoding
                delete cstarts; delete cends;
                split($9, cstarts, ",");
                split($10, cends, ",");
                name=$6"::"$7
                strand=$8;
                if(strand == "+"){
                    for(i=1; i < length(cstarts); i++){
                        # if the start of the exon is >= the cdsStart...
                        if(cends[i] >= $4){
                            # account for UTR? this just prints entire exon...
                            # could use cdsStart instead of cstarts[i]
                            print $1,cstarts[i],cends[i],name,strand
                            break;
                        }
                    }
                }
                else if(strand == "-"){
                    for(i=length(cstarts) - 1; i > 0; i--){
                        if(cstarts[i] <= $5){
                            # could use cdsEnd instead of cends[i]
                            print $1,cstarts[i],cends[i],name,strand
                            break;
                        }
                    }
                }
 
            }' > first.coding.exon.bed
Farhat commented

You can make it a tiny bit more efficient by using else instead of a second if in the first query processing.

brentp commented

@Farhat I changed it, but, yeah, I think it will be unnoticeable.

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