Commit abd6112a authored by Eric Coissac's avatar Eric Coissac

Add management of partial sequences

parent 7e3ddd41
......@@ -24,6 +24,7 @@ normalization="yes"
irdetection="yes"
organism="no"
types="chloro"
partial=0
function usage {
echo "Usage:" ;
......@@ -52,12 +53,21 @@ function usage {
echo
echo ' -m | --mitochondrion'
echo ' Selects for the annotation of an animal mitochondrion genome'
echo
echo ' -p | --partial'
echo ' Indicates that the genome sequence is partial and therefore in several contigs'
exit $2
}
function fastaIterator() {
awk '/^>/ {if (seq) printf("%s\f",seq); seq=""} \
{if (seq) seq=seq"\n"; seq=seq $1} \
END {print seq}' "$1"
}
# options may be followed by one colon to indicate they have a required argument
if ! options=$(getopt -o t:o:icrmh -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,help -- "$@")
if ! options=$(getopt -o t:o:icrmhp -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,partial,help -- "$@")
then
# something went wrong, getopt will put out an error message for us
usage $0 1
......@@ -74,6 +84,7 @@ do
-c|--chloroplast) types="chloro" ;;
-r|--nuclear-rdna) types="nucrdna" ;;
-m|--mitochondrion) types="mito" ;;
-p|--partial) partial="1" ;;
-h|--help) usage $0 0;;
(--) shift; break;;
(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
......@@ -101,151 +112,211 @@ pushTmpDir ORG.organnot
rm -f ${LOG}
openLogFile ${LOG}
case "$types" in
chloro)
loginfo "Annotating a plant chloroplast genome..."
IFS=$'\f'
if [ "$irdetection"=="yes" ]; then
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."
for sequence in $(fastaIterator "${QUERY}") ; do
unset IFS
if [[ ! -z "${sequence}" ]] ; then
echo "${sequence}" > toannotate.fasta
seqid=$(awk '(NR==1) {print substr($1,2,1000)}' toannotate.fasta)
case "$types" in
chloro)
loginfo "Annotating a plant chloroplast genome..."
if [[ "$irdetection"=="yes" ]] && (( partial == 0 )) ; then
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
loginfo "Normalizing the structure of the Chloroplast sequence..."
loginfo " LSC + IRB + SSC + IRA"
${PROG_DIR}/detectors/normalize/bin/go_normalize.sh toannotate.fasta > "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
else
cat toannotate.fasta > "${RESULTS}.norm.fasta"
rm -f "${RESULTS}.annot"
touch "${RESULTS}.annot"
fi
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the CDS..."
tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
if (( partial == 0 )) ; then
topology="circular"
defline="plastid, complete genome"
else
topology="linear"
defline="plastid, partial sequence"
fi
;;
nucrdna)
loginfo "Annotating a plant rDNA cistron..."
loginfo "Normalizing the structure of the cistron sequence..."
${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh toannotate.fasta > "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/nucrrna/bin/go_nucrrna.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
topology="linear"
defline="18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2 and 28S rRNA gene"
;;
mito)
loginfo "Annotating an animal mitochondrial genome..."
logerror "Not yet implemented"
if (( partial == 0 )) ; then
topology="circular"
defline="mitochondrion, complete genome"
else
topology="linear"
defline="mitochondrion, partial sequence"
fi
exit 1
;;
*)
usage $0 1;;
esac
if [[ "${organism}" == "no" ]]; then
organism="{organism}"
else
organism="$(echo ${organism} | tr '_' ' ')"
fi
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
sl=$(seqlength "${RESULTS}.norm.fasta")
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Printing minimal header..."
echo "ID ${seqid}; ${seqid}; ${topology}; genomic DNA; XXX; XXX; ${sl} BP."
echo "XX"
echo "AC ${seqid};"
echo "DE ${organism} ${defline}."
echo "XX"
loginfo "Done."
loginfo "Annotating the CDS..."
tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Printing annotations header..."
echo "FH Key Location/Qualifiers"
loginfo "Done."
loginfo "Printing the source feature"
echo "FT source 1..${sl}" >> "${RESULTS}.annot"
if [[ "${organism}" != "{organism}" ]] ; then
echo "FT /organism=\"${organism}\"" >> "${RESULTS}.annot"
fi
case "${types}" in
chloro)
echo "FT /organelle=\"plastid:chloroplast\"" >> "${RESULTS}.annot"
;;
mito)
echo "FT /organelle=\"mitochondrion\"" >> "${RESULTS}.annot"
;;
*)
loginfo "Nuclear sequence"
;;
esac
echo "FT /mol_type=\"genomic DNA\"" >> "${RESULTS}.annot"
if [[ "${taxid}" != "no" ]] ; then
echo "FT /db_xref=\"taxon:${taxid}\"" >> "${RESULTS}.annot"
fi
# echo "FT /country=\"Poland: Bialowieza Forest\"" >> "${RESULTS}.annot"
loginfo "Done."
topology="circular"
defline="plastid, complete genome"
;;
nucrdna)
loginfo "Annotating a plant rDNA cistron..."
loginfo "Ordering annotations..."
awk '/^.....(misc|repeat|rRNA|tRNA|gene|source)/ { \
match($3,"[0-9][0-9]*"); \
pos=substr($3,RSTART,RLENGTH)*1000 + 1; \
print pos,$0; \
next} \
{ pos++; \
print pos,$0}' "${RESULTS}.annot" | \
sort -nk1 |\
awk '{ \
match($0,"^[0-9]* ");\
line=substr($0,RLENGTH+1);\
print line}'
loginfo "Done."
loginfo "Normalizing the structure of the cistron sequence..."
${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh ${QUERY} > "${RESULTS}.norm.fasta"
loginfo "Closing annotations table..."
echo "XX"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/nucrrna/bin/go_nucrrna.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Computing statistics on nucleotide usage..."
awk '! /^>/ { \
seq=toupper($0); \
gsub(" ","",seq); \
lseq=length(seq); \
for (i=0; i < lseq; i++) { \
freq[substr(seq,i,1)]++}\
} \
END { \
other=0; \
for (i in freq) { \
if (i!="A" && i!="C" && i!="G" && i!="T") {\
other+=freq[i] \
} \
}; \
print "SQ Sequence "\
(freq["A"]+freq["C"]+freq["G"]+freq["T"]+other) \
" BP; "\
freq["A"]" A; "\
freq["C"]" C; "\
freq["G"]" G; "\
freq["T"]" T; "\
other" other;" \
}' "${RESULTS}.norm.fasta"
loginfo "Done."
topology="linear"
defline="18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2 and 28S rRNA gene"
;;
mito)
loginfo "Annotating an animal mitochondrial genome..."
logerror "Not yet implemented"
topology="circular"
defline="mitochondrion, complete genome"
exit 1
;;
*)
usage $0 1;;
esac
if [[ "${organism}" == "no" ]]; then
organism="{organism}"
else
organism="$(echo ${organism} | tr '_' ' ')"
fi
loginfo "Printing minimal header..."
echo "ID XXX; XXX; ${topology}; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
echo "XX"
echo "AC XXX;"
echo "DE ${organism} ${defline}."
echo "XX"
loginfo "Done."
loginfo "Printing annotations header..."
echo "FH Key Location/Qualifiers"
loginfo "Done."
loginfo "Ordering annotations..."
awk '/^.....(misc|repeat|rRNA|tRNA|gene)/ { \
match($3,"[0-9][0-9]*"); \
pos=substr($3,RSTART,RLENGTH)*1000 + 1; \
print pos,$0; \
next} \
{ pos++; \
print pos,$0}' "${RESULTS}.annot" | \
sort -nk1 |\
awk '{ \
match($0,"^[0-9]* ");\
line=substr($0,RLENGTH+1);\
print line}'
loginfo "Done."
loginfo "Closing annotations table..."
echo "XX"
loginfo "Done."
loginfo "Computing statistics on nucleotide usage..."
awk '! /^>/ { \
seq=toupper($0); \
gsub(" ","",seq); \
lseq=length(seq); \
for (i=0; i < lseq; i++) { \
freq[substr(seq,i,1)]++}\
} \
END { \
other=0; \
for (i in freq) { \
if (i!="A" && i!="C" && i!="G" && i!="T") {\
other+=freq[i] \
} \
}; \
print "SQ Sequence "\
(freq["A"]+freq["C"]+freq["G"]+freq["T"]+other) \
" BP; "\
freq["A"]" A; "\
freq["C"]" C; "\
freq["G"]" G; "\
freq["T"]" T; "\
other" other;" \
}' "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Reformating sequences..."
lines=$(wc -l "${RESULTS}.norm.fasta" | awk '{print $1}')
awk -v lines=$lines ' \
! /^>/ { \
seq=tolower($0); \
gsub(" ","",seq); \
printf(" ") ;\
for (i=0; i < 6; i++) { \
f=substr(seq,i * 10, 10); \
pos+=length(f); \
f = f substr(" ",1,10-length(f)); \
printf("%s ",f) \
}; \
if (NR==lines) \
{pos-=1}; \
printf(" %6d\n",pos) \
}' "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Closing sequence part..."
echo "//"
loginfo "Done."
loginfo "Reformating sequences..."
lines=$(wc -l "${RESULTS}.norm.fasta" | awk '{print $1}')
awk -v lines=$lines ' \
! /^>/ { \
seq=tolower($0); \
gsub(" ","",seq); \
printf(" ") ;\
for (i=0; i < 6; i++) { \
f=substr(seq,i * 10, 10); \
pos+=length(f); \
f = f substr(" ",1,10-length(f)); \
printf("%s ",f) \
}; \
if (NR==lines) \
{pos-=1}; \
printf(" %6d\n",pos) \
}' "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Closing sequence part..."
echo "//"
loginfo "Done."
fi
IFS=$'\f'
done # End of the loop over the sequences
popTmpDir
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