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Switch to a swissprot based reference database for CDS annotation

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Former-commit-id: 3da31ce8a135394ecac041291134d61f11f06d8f
Former-commit-id: 406f41a7cb2db14ea832480b86f72a11d3b0ab4a
This commit is contained in:
Eric Coissac
2022-02-16 22:50:17 +01:00
parent 90b3ee9b04
commit 831669433e
644 changed files with 25433 additions and 485597 deletions
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7
detectors/normalize/tools/extract_refLSC.sh
View File

@ -1,8 +1,13 @@
#!/bin/bash
#
# -- CAUTION -- Works as long than the script
# is not called through a symlink
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/../../../scripts/bash_init.sh"
gawk 'function printfasta(seq) { \
$AwkCmd 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \

7
detectors/normalize/tools/extract_refSSC.sh
View File

@ -1,8 +1,13 @@
#!/bin/bash
#
# -- CAUTION -- Works as long than the script
# is not called through a symlink
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/../../../scripts/bash_init.sh"
gawk 'function printfasta(seq) { \
$AwkCmd 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \

7
detectors/normalize/tools/selectViridiplantae.sh
View File

@ -1,5 +1,10 @@
#!/bin/bash
# -- CAUTION -- Works as long than the script
# is not called through a symlink
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/../../../scripts/bash_init.sh"
( \
for f in $* ; do \
@ -12,7 +17,7 @@
done \
) | \
grep -B 1 Viridiplantae | \
gawk '{print $1}' | \
$AwkCmd '{print $1}' | \
grep '\.gbk' | \
sed -E 's/(^.*\.gbk(.gz)?).$/\1/' | \
uniq