Hello, I have a fasta file with lines of format -
>FBti0019256 type=transposable_element; loc=2L:22300300..22304444; name=invader2{}555; dbxref=FlyBase_Annotation_IDs:TE19256,FlyBase:FBti0019256; MD5=d9259a0e33aad699215e64916bd47a5b; length=4145; release=r6.19; species=Dmel;
I would like to convert these lines into a bed file of format -
chr2L /t 22300300 /t 22304444 /t invader2
Is there a program that can directly perform this conversion or an awk command that can do this easier? Please let me know, thank you for your help.
3 answers
use an associative array in awk to store each component.
I'm just too lazy to extract the chrom/start/end, you get the idea.
awk -F ' ' '/^>/ {delete map;for(i=1;i<=NF;i++) {eq=index($i,"=");if(eq==0) continue;key=substr($i,1,eq-1);val=substr($i,eq+1); gsub(/;$/,"",val); map[key]=val;} OFS="\t"; print map["loc"],map["type"],map["name"],map["dbxref"],map["MD5"];}'
Assumption is that chromosomes are numbered, no x and y chromosomes. For fasta headers only, user can use grep
$ sed 's/.*loc.\(\b.*\b\):\(\b.*\b\)\.\.\(\b.*\b\);.*=\(\b.*\b\){.*/chr\1\t\2\t\3\t\4/g' test.txt
chr2L 22300300 22304444 invader2
$ cut -f2,3 -d";" test.txt| cut -d= -f2,3 | awk -v OFS="\t" -F':|=|;|\\..|{' '{print "chr"$1,$2,$3,$5}'
chr2L 22300300 22304444 invader2
$ cat test.txt
>FBti0019256 type=transposable_element; loc=2L:22300300..22304444; name=invader2{}555; dbxref=FlyBase_Annotation_IDs:TE19256,FlyBase:FBti0019256; MD5=d9259a0e33aad699215e64916bd47a5b; length=4145; release=r6.19; species=Dmel;
1000 bash cuts:
$ cut -f2,3 -d";" test.txt| cut -d= -f2,3 | cut -f1,2 -d: --output-delimiter=$'\t'| cut -f1,2,3 -d'.' --output-delimiter=$'\t' | cut -f1,2 -d';' --output-delimiter=$'\t'| cut -f1,2 -d'=' --output-delimiter=$'\t' | cut -f1,2 -d'{' --output-delimiter=$'\t'| cut -f1,2,3,4,6
2L 22300300 22304444 invader2
Actually, I think @ Daniel's one is best awk solution for OP requirement. In line with @Daniel's solution below, following awk solution is better than one using two cuts above :).
$ awk -v OFS="\t" -F';|=|:|\\..|{' '/^>/ {print "chr"$4,$5,$6,$8}' test.txt
chr2L 22300300 22304444 invader2
input:
>FBti0019256 type=transposable_element; loc=2L:22300300..22304444; name=invader2{}555; dbxref=FlyBase_Annotation_IDs:TE19256,FlyBase:FBti0019256; MD5=d9259a0e33aad699215e64916bd47a5b; length=4145; release=r6.19; species=Dmel;
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