From 0039402f180fb193f9260b1e29ae8182a6f2b1c6 Mon Sep 17 00:00:00 2001
From: criscuol <alexis.criscuolo@pasteur.fr>
Date: Wed, 24 Mar 2021 17:21:36 +0100
Subject: [PATCH] 2.01
---
README.md | 1 +
contig_info.sh | 28 ++++++++++------------------
2 files changed, 11 insertions(+), 18 deletions(-)
diff --git a/README.md b/README.md
index 40c4344..5109a11 100644
--- a/README.md
+++ b/README.md
@@ -50,6 +50,7 @@ Run _contig_info_ without option to read the following documentation:
-r residue content statistics for each contig sequence instead of
global statistics
-t tab-delimited output
+ -h prints this help and exits
```
## Examples
diff --git a/contig_info.sh b/contig_info.sh
index a853673..14a059d 100755
--- a/contig_info.sh
+++ b/contig_info.sh
@@ -32,7 +32,11 @@
# = VERSIONS = #
# ============ #
# #
- VERSION=2.0.210315ac #
+ VERSION=2.01.210324ac #
+# + modified temp file creation using TMPDIR variable #
+# + adding option -h #
+# #
+# VERSION=2.0.210315ac #
# + adding option -r #
# + adding trap when interrupting script #
# #
@@ -70,7 +74,7 @@
# ================ #
# #
# #
-if [ "$1" = "-?" ] || [ $# -lt 1 ]
+if [ "$1" == "-h" ] || [ $# -lt 1 ]
then
echo -e "\n\033[1m contig_info v$VERSION $COPYRIGHT\033[0m";
cat <<EOF
@@ -86,25 +90,14 @@ then
-r residue content statistics for each contig sequence instead of
global statistics
-t tab-delimited output
+ -h prints this help and exits
EOF
- exit ;
+ [ "$1" == "-h" ] && exit 0 || exit 1 ;
fi
# #
#############################################################################################################
-#############################################################################################################
-# #
-# ================ #
-# = CONSTANTS = #
-# ================ #
-# #
-# = temp directory ======================================================================================= #
-# #
- TEMP_DIR=${TMPDIR:-/tmp};
-# #
-#############################################################################################################
-
#############################################################################################################
# #
# ================ #
@@ -112,11 +105,10 @@ fi
# ================ #
# #
# = randomfile() ========================================================================================= #
-# returns a random file name within /tmp/ #
+# creates a random file within $TEMP_DIR and returns its name #
# #
randomfile() {
- rdmf=$TEMP_DIR/$RANDOM; while [ -e $rdmf ]; do rdmf=$TEMP_DIR/$RANDOM ; done
- echo $rdmf ;
+ echo $(mktemp -t -p ${TMPDIR:-/tmp}) ;
}
# #
#############################################################################################################
--
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