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Switch from awk to gawk

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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
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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
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@ -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
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@ -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
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@ -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
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@ -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); \