Patch bug in the inverted repeats annotation
Realize the annotation on the normalized chromosome Former-commit-id: 73e4e016d7bfe23fc92e4071efb0a4629eb8e21f Former-commit-id: d44249c0d078d475ca80386bb428fb660289b0dd
This commit is contained in:
@ -100,7 +100,7 @@ pushTmpDir ORG.normalize
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tmpLSC="tmp_$$_LSC.fasta"
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tmpSSC="tmp_$$_SSC.fasta"
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# Extract the first SC present in between the two IRs
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# Extract the central SC present in between the two IRs
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# considering it as LSC
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let "beginLSC=$endIR1+1"
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@ -110,7 +110,7 @@ pushTmpDir ORG.normalize
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strandLSC="${IR[1]}"
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# Extract the second SC present in two parts
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# Extract the external SC present in two parts
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# Considering it as SSC
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let "beginSSC=$endIR2+1"
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@ -130,16 +130,17 @@ pushTmpDir ORG.normalize
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# Actually this is the oposite LSC is SSC and SSC is LSC
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# Exchange the SSC and LSC sequences
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# Exchanges the SSC and LSC sequences
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mv ${tmpSSC} ${tmpfasta1}
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mv ${tmpLSC} ${tmpSSC}
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mv ${tmpfasta1} ${tmpLSC}
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# Exchange the IRa and IRb sequences
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# Exchanges the IRa and IRb sequences
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mv ${tmpIR1} ${tmpfasta1}
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mv ${tmpIR2} ${tmpIR1}
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mv ${tmpfasta1} ${tmpIR2}
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# Exchanges the strand of both the Single copies
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tmp=${strandSSC}
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strandSSC=${strandLSC}
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strandLSC=${tmp}
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@ -161,7 +162,7 @@ pushTmpDir ORG.normalize
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# Merges the four parts of the genome.
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cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
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exit 1
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popTmpDir
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@ -12,6 +12,15 @@ function lookForIR {
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local REPEATS="${MATCHES/.*/}.repseek"
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# Blast columns:
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# query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
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# We keep blast matches if :
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# The match is longer than 1000
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# The identity is higher than 80%
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#
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# The match file has the following format:
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# LSC/SSC begin end same_strand=1/diff_strand=0
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loginfo "Locating SSC and LSC by similarity..."
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blastn -db ${SCDB} \
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-query ${QUERY} \
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@ -31,7 +40,7 @@ function lookForIR {
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repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
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loginfo " --> $(wc -l ${REPEATS} | awk '{print $1}') repeats identified"
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loginfo "Done"
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loginfo "Marking and selecting the best inverted repeat..."
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local IR=( $(${SELECTIR} ${MATCHES} ${REPEATS}) )
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loginfo "Done"
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@ -8,6 +8,12 @@ repeats = open(sys.argv[2])
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chloro = {'LSC' : [], 'SSC' : [] }
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chlorosize =0
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# We scan the blast matches:
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# We build a vector with one position per base pair counting the matches
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# The match file has the following format:
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# LSC/SSC begin end same_strand=1/diff_strand=0
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for line in data:
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parts = line.strip().split()
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if len(parts) >= 4:
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@ -16,7 +22,8 @@ for line in data:
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end = int(parts[2])
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direction = int(parts[3])
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# Change the code of the direction:
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# reverse complement = -1
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if direction==0:
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direction=-1
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@ -39,36 +46,53 @@ maxLSC = float(max(abs(n) for n in chloro['LSC']))
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chloro['SSC']=[n / maxSSC for n in chloro['SSC']]
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chloro['LSC']=[n / maxLSC for n in chloro['LSC']]
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scoreMax=0
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len1Max=0
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len2Max=0
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imax = len(chloro['LSC'])
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for line in repeats:
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parts = line.strip().split()
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# First repeat position and length
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# (position start at 0)
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pos1 = int(parts[1]) -1
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len1 = int(parts[3])
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# Second repeat position and length
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# (position start at 0)
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pos2 = int(parts[2]) -1
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len2 = int(parts[4])
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# Location of the central single copy
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# - in between the two IR -
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c_begin = min(pos1 + len1,imax)
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c_end = min(pos2,imax)
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# Location of the external single copy
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# - in between the two IR -
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o_max = min(pos1 ,imax)
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o_min = min(pos2 + len2, imax)
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c_lsc = sum(abs(chloro['LSC'][n]) for n in range(c_begin,c_end))
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c_ssc = sum(abs(chloro['SSC'][n]) for n in range(c_begin,c_end))
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# count of coherent matches for LSC and SSC on the central single copy
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c_lsc = abs(sum(chloro['LSC'][n] for n in range(c_begin,c_end)))
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c_ssc = abs(sum(chloro['SSC'][n] for n in range(c_begin,c_end)))
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o_lsc = sum(abs(chloro['LSC'][n]) for n in range(0,o_max))
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o_ssc = sum(abs(chloro['SSC'][n]) for n in range(0,o_max))
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# count of coherent matches for LSC and SSC on the external single copy
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# this score is in two parts before the first copy and after the second
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o_lsc = sum(chloro['LSC'][n] for n in range(0,o_max))
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o_ssc = sum(chloro['SSC'][n] for n in range(0,o_max))
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o_lsc += sum(abs(chloro['LSC'][n]) for n in range(o_min,len(chloro['LSC'])))
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o_ssc += sum(abs(chloro['SSC'][n]) for n in range(o_min,len(chloro['SSC'])))
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o_lsc += sum(chloro['LSC'][n] for n in range(o_min,imax))
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o_ssc += sum(chloro['SSC'][n] for n in range(o_min,imax))
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o_lsc = abs(o_lsc)
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o_ssc = abs(o_ssc)
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c = float(c_lsc + c_ssc)
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o = float(o_lsc + o_ssc)
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if c > 0:
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c_lsc /= c
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c_ssc /= c
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@ -78,10 +102,9 @@ for line in repeats:
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o_ssc /= o
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score = ((c_lsc - c_ssc) ** 2 + (o_lsc - o_ssc) ** 2) / 2.0
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# print >>sys.stderr,"c.lsc = %f c.ssc = %f o.lsc = %f o.ssc = %f score = %6.4f (len=%d)" % (c_lsc,c_ssc,o_lsc,o_ssc,score,len1)
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if (score > scoreMax):
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if (score >= scoreMax) and ((len1 > len1Max) or (len2 > len2Max)):
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scoreMax = score
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pos1Max = pos1
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pos2Max = pos2
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@ -99,8 +122,8 @@ c_ssc = sum(chloro['SSC'][n] for n in range(c_begin,c_end))
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o_lsc = sum(chloro['LSC'][n] for n in range(0,o_max))
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o_ssc = sum(chloro['SSC'][n] for n in range(0,o_max))
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o_lsc += sum(chloro['LSC'][n] for n in range(o_min,len(chloro['LSC'])))
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o_ssc += sum(chloro['SSC'][n] for n in range(o_min,len(chloro['SSC'])))
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o_lsc += sum(chloro['LSC'][n] for n in range(o_min,imax))
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o_ssc += sum(chloro['SSC'][n] for n in range(o_min,imax))
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if abs(c_lsc) > abs(c_ssc):
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center = "LSC"
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@ -34,7 +34,7 @@ pushTmpDir ORG.organnot
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loginfo "Done."
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loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
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${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"
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${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the tRNA..."
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