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# requires "trTypes.txt" - a file with transcript types
# e.g. for Gencode GTF
# awk '$3=="transcript" {a=$0; gsub(/.*transcript_id "/,"",a);gsub(/".*/,"",a);;b=$0; gsub(/.*gene_type "/,"",b);gsub(/".*/,"",b); print a,b}' Gencode.gtf > trTypes.txt
BEGIN {
while (getline < "trTypes.txt") {
tT[$1]=$2;
};
OFS="\t";
rt[1]=0; #declare array
delete rt;
}
{
if ($1!=r) {
if (length(rt)==1) {#only if read overlaps one trType
for (tt in rt) {
if (tt=="") print r;
nT[tt]++;
};
};
delete rt;
r=$1;
};
if ($3 in tT) {
rt[tT[$3]]=1;
};
};
END {
for (tt in nT) {
print tt, nT[tt];
};
};
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