Very useful answer, thanks. I accepted Wen's solution because it is "ready to go".
• 0 views
•
link
Hello,
I would to know how to download the FASTAs of all the introns from a given UCSC genomic assembly.
The following command line prints all the introns of the ucsc/knownGene table.
$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" |\
gunzip -c |\
awk -F ' ' '{ exonCount=int($8);split($9,exonStarts,"[,]"); split($10,exonEnds,"[,]"); for(i=1;i<exonCount;i++) {printf("%s\t%s\t%s\t%s\t%s\tIntron_%d\n",$1,$2,$3,exonEnds[i],exonStarts[i+1],($3=="+"?i:exonCount-i));}}'
uc001aaa.3 chr1 + 12227 12612 Intron_1
uc001aaa.3 chr1 + 12721 13220 Intron_2
uc010nxq.1 chr1 + 12227 12594 Intron_1
uc010nxq.1 chr1 + 12721 13402 Intron_2
uc010nxr.1 chr1 + 12227 12645 Intron_1
uc010nxr.1 chr1 + 12697 13220 Intron_2
uc009vis.2 chr1 - 14829 14969 Intron_3
uc009vis.2 chr1 - 15038 15795 Intron_2
uc009vis.2 chr1 - 15942 16606 Intron_1
uc009vit.2 chr1 - 14829 14969 Intron_8
(...)
Very useful answer, thanks. I accepted Wen's solution because it is "ready to go".
Log in to answer this question.