Commit 14936719 authored by alain viari's avatar alain viari

Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate

parents d733a46f 6bd827ca
......@@ -118,9 +118,9 @@ INCDIR = $(abspath $(PRTDIR))/include
# default gmake variable in implicit rules
# ------------------------------------
CFLAGS = $(OPTIM) $(MACHDEF) -I$(INCDIR)
CFLAGS := $(CFLAGS) $(OPTIM) $(MACHDEF) -I$(INCDIR)
LDFLAGS = -L$(LIBDIR) -L.
LDFLAGS := $(LDFLAGS) -L$(LIBDIR) -L.
LDLIBS = $(LIBS) $(MALLOC_LIBS) $(MATH_LIBS) $(CC_LIBS)
......
......@@ -61,4 +61,4 @@ pushTmpDir ORG.ir
popTmpDir
exit 0
\ No newline at end of file
exit 0
......@@ -100,7 +100,7 @@ pushTmpDir ORG.normalize
tmpLSC="tmp_$$_LSC.fasta"
tmpSSC="tmp_$$_SSC.fasta"
# Extract the first SC present in between the two IRs
# Extract the central SC present in between the two IRs
# considering it as LSC
let "beginLSC=$endIR1+1"
......@@ -110,7 +110,7 @@ pushTmpDir ORG.normalize
strandLSC="${IR[1]}"
# Extract the second SC present in two parts
# Extract the external SC present in two parts
# Considering it as SSC
let "beginSSC=$endIR2+1"
......@@ -130,16 +130,17 @@ pushTmpDir ORG.normalize
# Actually this is the oposite LSC is SSC and SSC is LSC
# Exchange the SSC and LSC sequences
# Exchanges the SSC and LSC sequences
mv ${tmpSSC} ${tmpfasta1}
mv ${tmpLSC} ${tmpSSC}
mv ${tmpfasta1} ${tmpLSC}
# Exchange the IRa and IRb sequences
# Exchanges the IRa and IRb sequences
mv ${tmpIR1} ${tmpfasta1}
mv ${tmpIR2} ${tmpIR1}
mv ${tmpfasta1} ${tmpIR2}
# Exchanges the strand of both the Single copies
tmp=${strandSSC}
strandSSC=${strandLSC}
strandLSC=${tmp}
......@@ -162,7 +163,6 @@ pushTmpDir ORG.normalize
cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
popTmpDir
exit 0
......
#!/bin/bash
source "${THIS_DIR}/../../../scripts/bash_init.sh"
SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
......@@ -10,12 +12,21 @@ function lookForIR {
local REPEATS="${MATCHES/.*/}.repseek"
# Blast columns:
# query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# We keep blast matches if :
# The match is longer than 1000
# The identity is higher than 80%
#
# The match file has the following format:
# LSC/SSC begin end same_strand=1/diff_strand=0
loginfo "Locating SSC and LSC by similarity..."
blastn -db ${SCDB} \
-query ${QUERY} \
-outfmt 6 \
-max_target_seqs 10000 | \
awk '($4 > 1000) && ($3>80) { \
awk '($4 > 100) && ($3>80) { \
SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10)); \
if ($7 < $8) \
{print substr($2,1,3),$7,$8,SAME} \
......@@ -23,12 +34,13 @@ function lookForIR {
{print substr($2,1,3),$8,$7,SAME}}' | \
sort -nk 2 > ${MATCHES}
loginfo "Done"
loginfo "Looking for long inverted repeats..."
repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
loginfo " --> $(wc -l ${REPEATS} | awk '{print $1}') repeats identified"
loginfo "Done"
loginfo "Marking and selecting the best inverted repeat..."
local IR=( $(${SELECTIR} ${MATCHES} ${REPEATS}) )
loginfo "Done"
......
......@@ -8,6 +8,12 @@ repeats = open(sys.argv[2])
chloro = {'LSC' : [], 'SSC' : [] }
chlorosize =0
# We scan the blast matches:
# We build a vector with one position per base pair counting the matches
# The match file has the following format:
# LSC/SSC begin end same_strand=1/diff_strand=0
for line in data:
parts = line.strip().split()
if len(parts) >= 4:
......@@ -16,7 +22,8 @@ for line in data:
end = int(parts[2])
direction = int(parts[3])
# Change the code of the direction:
# reverse complement = -1
if direction==0:
direction=-1
......@@ -32,43 +39,60 @@ for line in data:
for p in range(begin,end):
chr[p]+=direction
maxSSC = float(max(abs(n) for n in chloro['SSC']))
maxLSC = float(max(abs(n) for n in chloro['LSC']))
chloro['SSC']=[n / maxSSC for n in chloro['SSC']]
chloro['LSC']=[n / maxLSC for n in chloro['LSC']]
scoreMax=0
len1Max=0
len2Max=0
imax = len(chloro['LSC'])
for line in repeats:
parts = line.strip().split()
# First repeat position and length
# (position start at 0)
pos1 = int(parts[1]) -1
len1 = int(parts[3])
# Second repeat position and length
# (position start at 0)
pos2 = int(parts[2]) -1
len2 = int(parts[4])
# Location of the central single copy
# - in between the two IR -
c_begin = min(pos1 + len1,imax)
c_end = min(pos2,imax)
# Location of the external single copy
# - in between the two IR -
o_max = min(pos1 ,imax)
o_min = min(pos2 + len2, imax)
c_lsc = sum(abs(chloro['LSC'][n]) for n in range(c_begin,c_end))
c_ssc = sum(abs(chloro['SSC'][n]) for n in range(c_begin,c_end))
# count of coherent matches for LSC and SSC on the central single copy
c_lsc = abs(sum(chloro['LSC'][n] for n in range(c_begin,c_end)))
c_ssc = abs(sum(chloro['SSC'][n] for n in range(c_begin,c_end)))
o_lsc = sum(abs(chloro['LSC'][n]) for n in range(0,o_max))
o_ssc = sum(abs(chloro['SSC'][n]) for n in range(0,o_max))
# count of coherent matches for LSC and SSC on the external single copy
# this score is in two parts before the first copy and after the second
o_lsc = sum(chloro['LSC'][n] for n in range(0,o_max))
o_ssc = sum(chloro['SSC'][n] for n in range(0,o_max))
o_lsc += sum(abs(chloro['LSC'][n]) for n in range(o_min,len(chloro['LSC'])))
o_ssc += sum(abs(chloro['SSC'][n]) for n in range(o_min,len(chloro['SSC'])))
o_lsc += sum(chloro['LSC'][n] for n in range(o_min,imax))
o_ssc += sum(chloro['SSC'][n] for n in range(o_min,imax))
o_lsc = abs(o_lsc)
o_ssc = abs(o_ssc)
c = float(c_lsc + c_ssc)
o = float(o_lsc + o_ssc)
if c > 0:
c_lsc /= c
c_ssc /= c
......@@ -78,10 +102,9 @@ for line in repeats:
o_ssc /= o
score = ((c_lsc - c_ssc) ** 2 + (o_lsc - o_ssc) ** 2) / 2.0
# 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)
if (score > scoreMax):
if (score >= scoreMax) and ((len1 > len1Max) or (len2 > len2Max)):
scoreMax = score
pos1Max = pos1
pos2Max = pos2
......@@ -99,8 +122,8 @@ c_ssc = sum(chloro['SSC'][n] for n in range(c_begin,c_end))
o_lsc = sum(chloro['LSC'][n] for n in range(0,o_max))
o_ssc = sum(chloro['SSC'][n] for n in range(0,o_max))
o_lsc += sum(chloro['LSC'][n] for n in range(o_min,len(chloro['LSC'])))
o_ssc += sum(chloro['SSC'][n] for n in range(o_min,len(chloro['SSC'])))
o_lsc += sum(chloro['LSC'][n] for n in range(o_min,imax))
o_ssc += sum(chloro['SSC'][n] for n in range(o_min,imax))
if abs(c_lsc) > abs(c_ssc):
center = "LSC"
......@@ -132,4 +155,4 @@ sys.stdout.write("%s %s %s %s %d %d %d %d %6.5f\n" % (center,
#for p in range(chlorosize):
# sys.stdout.write("%d %d %d\n" % (p,chloro['SSC'][p],chloro['LSC'][p]))
\ No newline at end of file
......@@ -33,7 +33,7 @@ pushTmpDir ORG.trna
TRNA=$(basename ${QUERY})
aragorn -i -w -seq ${QUERY} | \
${PROG_DIR}/../lib/aragorn_wrapper.awk
${AwkCmd} -f ${PROG_DIR}/../lib/aragorn_wrapper.awk
popTmpDir
......
......@@ -34,19 +34,19 @@ pushTmpDir ORG.organnot
loginfo "Done."
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh ${QUERY} >> "${RESULTS}.annot"
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the CDS..."
${PROG_DIR}/detectors/cds/bin/go_cds.sh ${QUERY} >> "${RESULTS}.annot"
${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Printing annotations header..."
......@@ -96,11 +96,11 @@ pushTmpDir ORG.organnot
freq["G"]" G; "\
freq["T"]" T; "\
other" other;" \
}' ${QUERY}
}' "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Reformating sequences..."
lines=$(wc -l ${QUERY} | awk '{print $1}')
lines=$(wc -l "${RESULTS}.norm.fasta" | awk '{print $1}')
awk -v lines=$lines ' \
! /^>/ { \
seq=tolower($0); \
......@@ -115,7 +115,7 @@ pushTmpDir ORG.organnot
if (NR==lines) \
{pos-=1}; \
printf(" %6d\n",pos) \
}' ${QUERY}
}' "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Closing sequence part..."
......
......@@ -19,7 +19,7 @@ function getAbsolutePath {
# Manage temp directory
function pushTmpDir {
TMP_DIR=$(mktemp -d -t "$1_proc_$$_")
TMP_DIR=$(mktemp -d -t "$1_proc_$$_XXXXXX")
pushd $TMP_DIR >& /dev/null
TMP_DIR_STACK="$TMP_DIR $TMP_DIR_STACK"
logdebug "Pushing temp directory $TMP_DIR"
......
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