Commit f58f9d67 authored by Eric Coissac's avatar Eric Coissac

Add the reformating of the sequence in EMBL format

parent f2a75cf9
......@@ -36,12 +36,92 @@ pushTmpDir ORG.organnot
rm -f ${LOG}
openLogFile ${LOG}
${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
loginfo "Normalizing the structure of the Chloroplast sequence..."
loginfo " LSC + IRB + SSC + IRA"
${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
loginfo "Done."
${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"
${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"
loginfo "Done."
cat "${RESULTS}.annot"
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Printing annotations header..."
echo "XX"
echo "FH Key Location/Qualifiers"
loginfo "Done."
loginfo "Ordering annotations..."
awk '/^.....[^ ]/ { \
match($3,"[0-9][0-9]*"); \
pos=substr($3,RSTART,RLENGTH)*1000 + 1; \
print pos,$0} \
/^..... / { \
pos++; \
print pos,$0}' "${RESULTS}.annot" | \
sort -nk1 | \
awk '{ \
match($0,"^[0-9]* ");\
line=substr($0,RLENGTH+1,100000);\
print line}'
loginfo "Done."
loginfo "Closing annotations table..."
echo "XX"
loginfo "Done."
loginfo "Computing statistics on nucleotide usage..."
awk '! /^>/ { \
seq=toupper($0); \
gsub(" ","",seq); \
lseq=length(seq); \
for (i=0; i < lseq; i++) { \
freq[substr(seq,i,1)]++}\
} \
END { \
other=0; \
for (i in freq) { \
if (i!="A" && i!="C" && i!="G" && i!="T") {\
other+=freq[i] \
} \
}; \
print "SQ Sequence "\
(freq["A"]+freq["C"]+freq["G"]+freq["T"]+other) \
" BP; "\
freq["A"]" A; "\
freq["C"]" C; "\
freq["G"]" G; "\
freq["T"]" T; "\
other" other;" \
}' ${QUERY}
loginfo "Done."
loginfo "Reformating sequences..."
lines=$(wc -l ${QUERY} | awk '{print $1}')
awk -v lines=$lines ' \
! /^>/ { \
seq=tolower($0); \
gsub(" ","",seq); \
printf(" ") ;\
for (i=0; i < 6; i++) { \
f=substr(seq,i * 10, 10); \
pos+=length(f); \
f = f substr(" ",1,10-length(f)); \
printf("%s ",f) \
}; \
if (NR==lines) \
{pos-=1}; \
printf(" %6d\n",pos) \
}' ${QUERY}
loginfo "Done."
loginfo "Closing sequence part..."
echo "//"
loginfo "Done."
popTmpDir
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