Add management of partial sequences

Former-commit-id: abd6112ac558592616c197f2fe761880a847b031
Former-commit-id: d2ea2e7e306512bf8ef92d3497a0302919b81010

org-annotate.sh

@@ -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;;
@@ -101,22 +112,34 @@ pushTmpDir ORG.organnot
 	rm -f ${LOG}
 	openLogFile ${LOG}
 
+	IFS=$'\f'
+	
+	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 [ "$irdetection"=="yes" ]; then
+					if [[ "$irdetection"=="yes" ]] && (( partial == 0 )) ; 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"
+							${PROG_DIR}/detectors/normalize/bin/go_normalize.sh toannotate.fasta > "${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..."
@@ -131,14 +154,20 @@ pushTmpDir ORG.organnot
 						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 ${QUERY} > "${RESULTS}.norm.fasta"
+						${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh toannotate.fasta > "${RESULTS}.norm.fasta"
 					loginfo "Done."
 					
 					loginfo "Annotating the rRNA genes..."
@@ -148,15 +177,22 @@ pushTmpDir ORG.organnot
 					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 $0 1;;
 			esac
@@ -167,10 +203,12 @@ pushTmpDir ORG.organnot
 				organism="$(echo ${organism} | tr '_' ' ')"
 			fi
 			
+			sl=$(seqlength "${RESULTS}.norm.fasta")
+			
 			loginfo "Printing minimal header..."		
-		echo "ID   XXX; XXX; ${topology}; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
+				echo "ID   ${seqid}; ${seqid}; ${topology}; genomic DNA; XXX; XXX; ${sl} BP."
 				echo "XX"
-		echo "AC   XXX;"
+				echo "AC   ${seqid};"
 				echo "DE   ${organism} ${defline}."
 				echo "XX"
 			loginfo "Done."
@@ -179,8 +217,36 @@ pushTmpDir ORG.organnot
 		    	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."
+			
 			loginfo "Ordering annotations..."
-		awk '/^.....(misc|repeat|rRNA|tRNA|gene)/ { \
+				awk '/^.....(misc|repeat|rRNA|tRNA|gene|source)/ { \
 				        match($3,"[0-9][0-9]*"); \
 				        pos=substr($3,RSTART,RLENGTH)*1000 + 1; \
 				        print pos,$0;    \
@@ -194,6 +260,8 @@ pushTmpDir ORG.organnot
 				        print line}' 
 			loginfo "Done."
 			
+			
+			
 			loginfo "Closing annotations table..."
 				echo "XX"
 			loginfo "Done."
@@ -246,6 +314,9 @@ pushTmpDir ORG.organnot
 			loginfo "Closing sequence part..."
 				echo "//"
 			loginfo "Done."
+		fi
 		
+		IFS=$'\f'
+	done # End of the loop over the sequences
 popTmpDir