is the following correct to save the script
Code :
awk '
BEGIN { print "gene ID CHROM POS txstart txend"
}
FNR == 1 {
next
}
FNR == NR {
POS[++k] = $2
ID[k] = $3
next
}
{ for(i = 1; i <= k; i++)
if(POS[i] >= $5 && POS[i] <= $6)
print $1, ID[i], $3, POS[i], $5, $6
}' pre_snpinfo_tumor.txt refFlat.txt > data.txt
if yes the od -bs < data.txt gave me
0000000
for 3) I got
Code :
awk '
> BEGIN {print "gene ID CHROM POS txstart txend"
> }
> FNR == 1 {
> next
> }
> FNR == NR {
> POS[++k] = $2
> ID[k] = $3
> next
> }
> {for(i = 1; i <= k; i++)
>
annotation.vcf out.txt
annovar.latest.tar plink-1.07-i686/
A_thaliana_Jun_2009.2bit plink-1.07-i686.zip
.bash_history plink-1.07-i868
bedtools2/ pre_snpinfo_normal.txt
bedtools-2.25.0.tar.gz pre_snpinfo_tumor1.txt
bedtools-2.25.0.tar.gz.1 Pre_snpinfo_tumor1.txt
bin/ pre_snpinfo_tumor2.txt
bposition.txt pre_snpinfo_tumor.txt
BRCA/ pre_snpinfo_tumor.txt.bak
BRCA_gene_RSEM.txt pre_snp_normal.txt
BRCA_SNP6.normal.gt pre_snp_tumor1.txt
BRCA_SNP6.tumor.gt pre_snp_tumor2.txt
.ccache/ pre_snp_tumor3.txt
clinvar.vcf pre_snp_tumor.txt
datasnp R/
datasnp.rtf .RDataTmp
datasnp.txt refFlat.txt
data.tumor .Renviron
data.tumor.txt rminer_1.4.2.tar.gz
datatumor.txt rminer_1.4.2.tar.gz.1
data.txt short1_pre_snp_tumor.txt
dd.txt short2_gwas.map
dn.txt short2_gwas.ped
dt.txt short2_pre_snp_tumor.txt
.emacs snpanno
geneinfo-3.txt snpEff/
geneinfo_normal.txt snpEff_latest_core.zip
gene_normal.txt snpinfo_normal.txt
gene.rtf snpinfo_tumor.txt
.gnome2/ snp_normal.txt
gwas.map snp_tumor.txt
gwas.ped .ssh/
index.html temp
.kshrc test.chr22.ann.vcf
.mkshrc transpose-2.0/
.mozilla/ transpose-2.0.zip
nohup.out tumor.exp.gt.txt
normal.exp.gt.txt .viminfo
out1.txt .zshrc
out_file
> >= $5 && POS[i] <= $6)
>
annotation.vcf out.txt
annovar.latest.tar plink-1.07-i686/
A_thaliana_Jun_2009.2bit plink-1.07-i686.zip
.bash_history plink-1.07-i868
bedtools2/ pre_snpinfo_normal.txt
bedtools-2.25.0.tar.gz pre_snpinfo_tumor1.txt
bedtools-2.25.0.tar.gz.1 Pre_snpinfo_tumor1.txt
bin/ pre_snpinfo_tumor2.txt
bposition.txt pre_snpinfo_tumor.txt
BRCA/ pre_snpinfo_tumor.txt.bak
BRCA_gene_RSEM.txt pre_snp_normal.txt
BRCA_SNP6.normal.gt pre_snp_tumor1.txt
BRCA_SNP6.tumor.gt pre_snp_tumor2.txt
.ccache/ pre_snp_tumor3.txt
clinvar.vcf pre_snp_tumor.txt
datasnp R/
datasnp.rtf .RDataTmp
datasnp.txt refFlat.txt
data.tumor .Renviron
data.tumor.txt rminer_1.4.2.tar.gz
datatumor.txt rminer_1.4.2.tar.gz.1
data.txt short1_pre_snp_tumor.txt
dd.txt short2_gwas.map
> t $1, ID[i], $3, POS[i], $5, $6
> }' pre_snpinfo_tumor.txt refFlat.txt > data.txt
awk: cmd. line:12: >= $5 && POS[i] <= $6)
awk: cmd. line:12: ^ syntax error
awk: cmd. line:12: >= $5 && POS[i] <= $6)
awk: cmd. line:12: ^ syntax error
awk: cmd. line:13: t $1, ID[i], $3, POS[i], $5, $6
awk: cmd. line:13: ^ syntax error
awk: cmd. line:13: t $1, ID[i], $3, POS[i], $5, $6
awk: cmd. line:13: ^ syntax error
awk: cmd. line:13: t $1, ID[i], $3, POS[i], $5, $6
awk: cmd. line:13: ^ syntax error
---------- Post updated at 02:04 AM ---------- Previous update was at 01:29 AM ----------
i have a question does unix knows that CHOM, POS, ID are the header
like in R we type in read.table (" file,header=TRUE")
because I added the header ...the data was with no header (snp data)
so I wonder if it understand that those are the header