Rename file in directory using contents within each file
In the below there are two generic .vcf files (genome.S1.vcf and genome.S2.vcf) in a directory. There wont always be two genaric files but I am trying to use bash to rename each of these generic files with specfic text (unique identifier) within in each .vcf. The text will always be different, but it will always be in the same position (after the word FORMAT) on the same line (that starts with #). Each .vcf is tab-delimited, not sure if my attempt is the best way, but hopefully it helps. Thank you .
genome.S1.vcf
Code:
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##FILTER=<ID=NotGenotyped,Description="Locus contains forcedGT input alleles which could not be genotyped">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NAME1_S1
chr10 323215 . A . . LowGQX END=323313;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0
chr10 323314 . C . . LowGQX;LowDepth END=323397;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:3:1:0:1
genome.S2.vcf
Code:
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##FILTER=<ID=NotGenotyped,Description="Locus contains forcedGT input alleles which could not be genotyped">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 11-1111-ID_S5
chr10 323215 . A . . LowGQX END=323313;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0
chr10 323314 . C . . LowGQX;LowDepth END=323385;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0
desired (each vcf in directory renamed with unique identifier)
NAME1_S1.vcf
Code:
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...
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##FILTER=<ID=NotGenotyped,Description="Locus contains forcedGT input alleles which could not be genotyped">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NAME1_S1
chr10 323215 . A . . LowGQX END=323313;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0
chr10 323314 . C . . LowGQX;LowDepth END=323397;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP 0/0:3:1:0:1
11-1111-ID_S5.vcf
Code:
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...
...
##FILTER=<ID=NotGenotyped,Description="Locus contains forcedGT input alleles which could not be genotyped">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 11-1111-ID_S5
chr10 323215 . A . . LowGQX END=323313;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0
chr10 323314 . C . . LowGQX;LowDepth END=323385;BLOCKAVG_min30p3a GT:GQX:DP:DPF:MIN_DP .:.:0:0:0
bash
Code:
cd /path/to/files
for f in *.vcf ; do # loop through all vcf files
new="$(head -1 "$f" | awk '{print $10}').vcf" # store value of $10 in new
if [ ! -f "$new" ]; then # if original file doesn't match new
echo -e Renaming $f to $new # log rename
mv "$f" "$new" # rename original to new
fi # close if
done # close loop
I am on a HP-UX machine I have a directory called "/u01/blobs" and the files look like this:
ls -1
7398
7399
7400
I need to produce a comma delimited file with the following format:
filename,location/filename
i.e:
7398,/u01/blobs/7398
7399,/u01/blobs/7399
7400,/u01/blobs/7400
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12-26-2019
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