Eric Coissac
37e1ecc9fd
Former-commit-id: 77fd69c9687bfc7cfd3305299c7c81d2a9eddada Former-commit-id: 4d09933673c30d6a9b2b9cc985b33ef23d7a99f4
51 lines
3.2 KiB
Bash
Executable File
51 lines
3.2 KiB
Bash
Executable File
#!/bin/bash
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#
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awk '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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/^LOCUS / {AC=$2; sequence=""; seqon=0; FROM="";TO=""} \
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/^ misc_feature/ {LOCUS=$2; STRAND=1} \
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/^ misc_feature/ && /complement/ {STRAND=0; \
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sub("complement\\(","",LOCUS); \
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sub("\\)","",LOCUS); \
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} \
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/large single copy/ && /LSC/ {split(LOCUS,POS,"."); \
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FROM=POS[1]; \
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TO=POS[3]; \
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LENGTH=TO-FROM+1 \
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} \
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/^ORIGIN/ {seqon=1} \
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/^ *[1-9][0-9]* [a-z ]+$/ && seqon {seq=$2 $3 $4 $5 $6 $7; \
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gsub("[^acgt]","n",seq);\
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sequence=sequence seq \
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} \
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/^\/\// && FROM && (LENGTH > 60000) && (LENGTH < 100000) \
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{print ">LSC_"AC" Strand="STRAND";", \
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"cut="FROM".."TO";", \
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"seq_length="LENGTH";"; \
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SS=substr(sequence,FROM,LENGTH); \
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if (! STRAND) \
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SS=revcomp(SS); \
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printfasta(SS); \
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} \
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' $*
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