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

14
scripts/bash_init.sh
View File

@ -3,6 +3,8 @@
# for setting up basic variables and functions
#
export AwkCmd="gawk"
########################
#
# General usage functions
@ -25,8 +27,8 @@ function pushTmpDir {
}
function popTmpDir {
TMP_DIR=$(echo $TMP_DIR_STACK | awk '{print $1}')
TMP_DIR_STACK=$(echo $TMP_DIR_STACK | awk '{$1="";print $0}')
TMP_DIR=$(echo $TMP_DIR_STACK | $AwkCmd '{print $1}')
TMP_DIR_STACK=$(echo $TMP_DIR_STACK | $AwkCmd '{$1="";print $0}')
popd >& /dev/null
rm -rf $TMP_DIR >& /dev/null
logdebug "Poping temp directory $TMP_DIR"
@ -91,7 +93,7 @@ function fastaCount {
function seqlength {
cat $1 | \
wc |\
awk -v t="`head -1 $1 | wc -c`" '{print $3 - t - $1 + 1}'
$AwkCmd -v t="`head -1 $1 | wc -c`" '{print $3 - t - $1 + 1}'
}
# extract a subseq from a fasta sequence
@ -99,7 +101,7 @@ function seqlength {
# - $2 : First position of the subsequence (first position is numered 1),
# - $3 : End of the subsequence (included in the subsequence)
function cutseq {
awk -v from=$2 -v end=$3 'function printfasta(seq) { \
$AwkCmd -v from=$2 -v end=$3 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \
@ -114,13 +116,13 @@ function cutseq {
# a single sequence
# - $1 : The fasta file containing the sequences to join
function joinfasta {
awk '(NR==1 && /^>/) {print $0} \
$AwkCmd '(NR==1 && /^>/) {print $0} \
! /^>/ {print $0}' $1 | \
formatfasta
}
function formatfasta {
awk 'function printfasta(seq) { \
$AwkCmd 'function printfasta(seq) { \
seqlen=length(seq); \
for (i=1; i <= seqlen; i+=60) \
print substr(seq,i,60); \