通过简单数据熟悉Linux下生物信息学各种操作3

efetch -db nucleotide -id NC_002549.1 -format gb > NC.gb
 ~/bin/readseq -format=GFF -o NC.gff NC.gb

cat NC.gff |awk '{print $1,$2,$3}'|head -5

##gff-version 2 
# seqname source
NC_002549 - source
NC_002549 - 5'UTR
NC_002549 - gene

cat NC.gff|cut -f 1,2,3|head -5

##gff-version 2
# seqname   source  feature
NC_002549   -   source
NC_002549   -   5'UTR
NC_002549   -   gene

cat NC.gff | awk ' { print $3, $5-$4 + 1 } ' | head -5

 1
source 1
source 18959
5'UTR 55
gene 2971

cat NC.gff|awk '$3=="CDS" {print $3,$5-$4+1,$9}'

CDS 2220 gene
CDS 1023 gene
CDS 981 gene
CDS 885 group
CDS 1146 group
CDS 1095 gene
CDS 884 group
CDS 10 group
CDS 867 gene
CDS 756 gene
CDS 6639 gene

cat NC.gff | awk '$3 =="gene" { len=$5-$4 + 1; size += len; print "Size:", size } '

cat NC.gff | awk '$3 =="gene" { len=$5-$4 + 1; size += len; print "Size:", size } '

Size: 2971
Size: 4347
Size: 5852
Size: 8258
Size: 9711
Size: 11345
Size: 18127

cat NC.gff | awk '$3 =="gene" { print $3, $5-$4 + 1, $9 } '

gene 2971 gene
gene 1376 gene
gene 1505 gene
gene 2406 gene
gene 1453 gene
gene 1634 gene
gene 6782 gene