PhyloSkims/annotate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Switch from awk to gawk

Browse Source 
Former-commit-id: 70b104ab89d4c90a35925dbbcacdafaf6c1f2836
Former-commit-id: bf29abf66345cbc0ca81461064dcca63dfd4c15c
This commit is contained in:
Eric Coissac
2015-11-08 19:33:00 +01:00
parent 6fa63daf3f
commit 2261fa1c48
16 changed files with 52 additions and 49 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
detectors/rrna/bin/go_rrna.sh
View File

@ -33,13 +33,13 @@ pushTmpDir ORG.rrna
RRNA=$(basename ${QUERY})
hmmsearch --max ${RRNADB} ${QUERY} | \
awk '/Query: / { \
$AwkCmd '/Query: / { \
profil=$2; \
match($3,"[0-9][0-9]*");\
lprof=substr($3,RSTART,RLENGTH)} \
/ [0-9][0-9]* ! / { \
print profil,lprof,$7,$8,$10,$11}' | \
awk '($3 <=5) && (($2-$4) <=5) { \
$AwkCmd '($3 <=5) && (($2-$4) <=5) { \
full=1;$5=$5-$3+1;$6=$6+($2-$4)}
{loc=$5".."$6} \
($1 ~ /_RC$/) { \

6
detectors/rrna/tools/buildRRNAModels.sh
View File

@ -11,7 +11,7 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
function fasta1li {
awk '/^>/ {if (sequence) \
$AwkCmd '/^>/ {if (sequence) \
{print sequence}; \
print $0; \
sequence=""} \
@ -28,7 +28,7 @@ function dereplicate {
grep -v -- -- | \
sed -E "s/count=[0-9]+; //" | \
sed 's/cluster_weight/count/' | \
awk ' /^>/ {SEQ++;\
$AwkCmd ' /^>/ {SEQ++;\
match($0,"count=[0-9][0-9]*;");\
count=substr($0,RSTART,RLENGTH);\
$1=$1"_"SEQ;\
@ -58,7 +58,7 @@ function clustering {
}
function revcomp {
awk 'function printfasta(seq) { \
$AwkCmd 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \

2
detectors/rrna/tools/extract_ref16S.sh
View File

@ -2,7 +2,7 @@
#
awk 'function printfasta(seq) { \
gawk 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \

2
detectors/rrna/tools/extract_ref23S.sh
View File

@ -2,7 +2,7 @@
#
awk 'function printfasta(seq) { \
gawk 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \

2
detectors/rrna/tools/extract_ref4.5S.sh
View File

@ -2,7 +2,7 @@
#
awk 'function printfasta(seq) { \
gawk 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \

2
detectors/rrna/tools/extract_ref5S.sh
View File

@ -2,7 +2,7 @@
#
awk 'function printfasta(seq) { \
gawk 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \

2
detectors/rrna/tools/revcomp_alignments.sh
View File

@ -11,7 +11,7 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
function revcomp {
awk 'function printfasta(seq) { \
gawk 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \