Eric Coissac
2261fa1c48
Former-commit-id: 70b104ab89d4c90a35925dbbcacdafaf6c1f2836 Former-commit-id: bf29abf66345cbc0ca81461064dcca63dfd4c15c
44 lines
2.3 KiB
Bash
44 lines
2.3 KiB
Bash
#!/bin/bash
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#
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# Reverse complement a fasta formated alignment
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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function revcomp {
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gawk 'function printfasta(seq) { \
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seqlen=length(seq); \
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for (i=1; i <= seqlen; i+=60) \
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print substr(seq,i,60); \
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} \
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function comp(seq) { \
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"echo "seq" | tr acgtACGT tgcaTGCA " | getline res; \
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close("echo "seq" | tr acgtACGT tgcaTGCA "); \
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return res; \
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} \
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function rev(seq) { \
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"echo "seq" | rev " | getline res; \
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close("echo "seq" | rev "); \
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return res; \
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} \
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function revcomp(seq) { \
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res=rev(comp(seq)); \
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return res; \
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} \
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\
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(seq) && /^>/ {print head; \
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printfasta(revcomp(seq)); \
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seq=""} \
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/^>/ {head=$0} \
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! /^>/ {seq=seq$0} \
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END { print head; \
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printfasta(revcomp(seq)); \
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}' $*
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}
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revcomp $* |