PhyloSkims/annotate
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Run the annotation on the normalized sequence

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Former-commit-id: 48e30ca5dff232ebf886d351cfd254b3fc3a0798
Former-commit-id: e4832b9fe1c644d232b6bc724ab98d5ee18ab6eb
This commit is contained in:
Eric Coissac
2015-11-09 15:34:59 +01:00
parent ae703c70d6
commit 58e99a81eb
1 changed files with 6 additions and 6 deletions
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12
org-annotate.sh
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@ -38,15 +38,15 @@ pushTmpDir ORG.organnot
loginfo "Done." loginfo "Done."
loginfo "Annotating the tRNA..." 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 "Done."
loginfo "Annotating the rRNA genes..." 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 "Done."
loginfo "Annotating the CDS..." 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 "Done."
loginfo "Printing annotations header..." loginfo "Printing annotations header..."
@ -96,11 +96,11 @@ pushTmpDir ORG.organnot
freq["G"]" G; "\ freq["G"]" G; "\
freq["T"]" T; "\ freq["T"]" T; "\
other" other;" \ other" other;" \
}' ${QUERY} }' "${RESULTS}.norm.fasta"
loginfo "Done." loginfo "Done."
loginfo "Reformating sequences..." loginfo "Reformating sequences..."
lines=$(wc -l ${QUERY} | awk '{print $1}') lines=$(wc -l "${RESULTS}.norm.fasta" | awk '{print $1}')
awk -v lines=$lines ' \ awk -v lines=$lines ' \
! /^>/ { \ ! /^>/ { \
seq=tolower($0); \ seq=tolower($0); \
@ -115,7 +115,7 @@ pushTmpDir ORG.organnot
if (NR==lines) \ if (NR==lines) \
{pos-=1}; \ {pos-=1}; \
printf(" %6d\n",pos) \ printf(" %6d\n",pos) \
}' ${QUERY} }' "${RESULTS}.norm.fasta"
loginfo "Done." loginfo "Done."
loginfo "Closing sequence part..." loginfo "Closing sequence part..."