diff --git a/README.md b/README.md
index 4c0efbb226d5b96a724c4abd7cc70666b02e9ac2..1bc63411c88b50b3d6a3865aaa8856c1b082000d 100644
--- a/README.md
+++ b/README.md
@@ -1,76 +1,82 @@
-
-#### DESCRIPTION
-
-Little bash Functions contains the 9 following functions:
-show_time_fun
-test_tab_in_file_fun
-test_space_in_file_fun
-space_replacement_in_file_fun
-file_pattern_detection_fun
-test_column_nb_perline_in_file_fun
-single_path_with_regex_fun
-var_existence_check_fun
-file_exten_verif_name_recov_fun
-
-
-#### LICENCE
-
-This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-Distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-See the GNU General Public License for more details at https://www.gnu.org/licenses.
-
-
-#### CREDITS
-
-Gael A. Millot, Hub-C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
-
-
-#### HOW TO USE IT
-
-Download the desired Tagged version, never the current master.
-
-To directly source a version in the environment:
-source <(curl -s https://gitlab.pasteur.fr/gmillot/little_bash_functions/raw/v1.0.0/little_bash_functions.sh)
-
-To directly save the little_bash_functions.sh file:
-wget https://gitlab.pasteur.fr/gmillot/little_bash_functions/raw/v1.0.0/little_bash_functions.sh
-
-To save all the files:
-wget https://gitlab.pasteur.fr/gmillot/little_bash_functions/-/archive/v1.0.0/little_bash_functions-v1.0.0.zip
-
-To source the local little_bash_functions.sh to have the functions available in the working environment:
-source /pasteur/homes/gmillot/Git_versions_to_use/little_bash_functions-v1.0.0/little_bash_functions.sh
-
-Description of the functions is at the beginning of the function body. To obtain it, read the little_bash_functions.sh
-
-
-#### FILE DESCRIPTIONS
-
-little_bash_functions.sh file that has to be sourced
-
-
-#### WEB LOCATION
-
-Check for updated versions (more recent release tags) at https://gitlab.pasteur.fr/gmillot/little_bash_functions/tags
-
-
-#### WHAT'S NEW IN
-
-## v1.3.0
-
-test_column_nb_perline_in_file_fun with better writting
-
-
-## v1.2.0
-
-output file name error in test_column_nb_perline_in_file_fun fixed
-
-
-## v1.1.0
-
-single_path_with_regex_fun function deals now with url
-
-
-## v1.0.0
-
-Everything
+
+#### DESCRIPTION
+
+Little bash Functions contains the 9 following functions:
+show_time_fun
+test_tab_in_file_fun
+test_space_in_file_fun
+space_replacement_in_file_fun
+file_pattern_detection_fun
+test_column_nb_perline_in_file_fun
+single_path_with_regex_fun
+var_existence_check_fun
+file_exten_verif_name_recov_fun
+
+
+#### LICENCE
+
+This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+Distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+See the GNU General Public License for more details at https://www.gnu.org/licenses.
+
+
+#### CREDITS
+
+Gael A. Millot, Hub-C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
+
+
+#### HOW TO USE IT
+
+Download the desired Tagged version, never the current master.
+
+To directly source a version in the environment:
+source <(curl -s https://gitlab.pasteur.fr/gmillot/little_bash_functions/raw/v1.0.0/little_bash_functions.sh)
+
+To directly save the little_bash_functions.sh file:
+wget https://gitlab.pasteur.fr/gmillot/little_bash_functions/raw/v1.0.0/little_bash_functions.sh
+
+To save all the files:
+wget https://gitlab.pasteur.fr/gmillot/little_bash_functions/-/archive/v1.0.0/little_bash_functions-v1.0.0.zip
+
+To source the local little_bash_functions.sh to have the functions available in the working environment:
+source /pasteur/homes/gmillot/Git_versions_to_use/little_bash_functions-v1.0.0/little_bash_functions.sh
+
+Description of the functions is at the beginning of the function body. To obtain it, read the little_bash_functions.sh
+
+
+#### FILE DESCRIPTIONS
+
+little_bash_functions.sh file that has to be sourced
+
+
+#### WEB LOCATION
+
+Check for updated versions (more recent release tags) at https://gitlab.pasteur.fr/gmillot/little_bash_functions/tags
+
+
+#### WHAT'S NEW IN
+
+
+## v2.0
+
+function modified because of return. echo $? cannot be used with. Use global variables as explained inside functions
+
+
+## v1.3.0
+
+test_column_nb_perline_in_file_fun with better writting
+
+
+## v1.2.0
+
+output file name error in test_column_nb_perline_in_file_fun fixed
+
+
+## v1.1.0
+
+single_path_with_regex_fun function deals now with url
+
+
+## v1.0.0
+
+Everything
diff --git a/little_bash_functions.sh b/little_bash_functions.sh
index 06a48195e00aeee5fc2a66c33c24c79c87b22b78..5de3ffe3e47ba9e767cd06844ecf3d4a45ce20f3 100644
--- a/little_bash_functions.sh
+++ b/little_bash_functions.sh
@@ -1,8 +1,8 @@
-#!/bin/bash # shebang
+#!/bin/bash -uel # shebang
################################################################
## ##
-## LITTLE BASH FUNCTIONS v1.3.0 ##
+## LITTLE BASH FUNCTIONS v2.0 ##
## ##
## Gael A. Millot ##
## ##
@@ -63,32 +63,38 @@ function show_time_fun () {
function test_tab_in_file_fun () {
# DESCRIPTION
# test if tabulations are present in a file
+ # WARNING
+ # I had to use a global variable file_pattern_detection_fun_RETURN and not a local one to be able to deal with the check.sh file in genetic_linkage project
# ARGUMENTS
# $0: name of the function
# $1: first argument, ie file name and path
# RETURN OUTPUT
- # 0: tabulation detected
- # 1: error in $1
- # 2: no tabulation detected
+ # test_tab_in_file_fun_RETURN=0: tabulation detected
+ # test_tab_in_file_fun_RETURN=1: error in $1
+ # test_tab_in_file_fun_RETURN=2: no tabulation detected
# EXAMPLES
# test_tab_in_file_fun /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/freq
# test_tab_in_file_fun /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/pedfile1.pro
# argument checking
if [[ -z $1 ]]; then
echo -e "\n### test_tab_in_file_fun ERROR ### ARGUMENT 1 REQUIRED\n"
- return 1
+ test_tab_in_file_fun_RETURN=1
+ return 0
fi
if [[ ! -f $1 ]]; then
echo -e "\n### test_tab_in_file_fun ERROR ### $1 FILE NOT PRESENT IN `dirname $1`\n"
- return 1
+ test_tab_in_file_fun_RETURN=1
+ return 0
fi
# main code
local TEMPO_TAB_COUNT=$(grep -o $'\t' $1 | wc -l) # for tabulation problem in bash and grep, see https://askubuntu.com/questions/53071/how-to-grep-for-tabs-without-using-literal-tabs-and-why-does-t-not-work
if [[ $TEMPO_TAB_COUNT == 0 ]] ; then
echo -e "\n### test_tab_in_file_fun ERROR: NO TABULATIONS DETECTED IN $1\n"
- return 2
+ test_tab_in_file_fun_RETURN=2
+ return 0
else
echo -e "\ntest_tab_in_file_fun MESSAGE: TABULATIONS DETECTED IN $1 AS EXPECTED\n"
+ test_tab_in_file_fun_RETURN=0
return 0
fi
}
@@ -98,32 +104,38 @@ function test_tab_in_file_fun () {
function test_space_in_file_fun () {
# DESCRIPTION
# test if spaces are present in a file
+ # WARNING
+ # I had to use a global variable file_pattern_detection_fun_RETURN and not a local one to be able to deal with the check.sh file in genetic_linkage project
# ARGUMENTS
# $0: name of the function
# $1: first argument, ie file name and path
# RETURN OUTPUT
- # 0: space detected
- # 1: error in $1
- # 2: no space detected
+ # test_space_in_file_fun_RETURN=0: space detected
+ # test_space_in_file_fun_RETURN=1: error in $1
+ # test_space_in_file_fun_RETURN=2: no space detected
# EXAMPLES
# test_space_in_file_fun /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/freq
# test_space_in_file_fun /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/pedfile1.pro
# argument checking
if [[ -z $1 ]]; then
echo -e "\n### test_space_in_file_fun ERROR ### ARGUMENT 1 REQUIRED\n"
- return 1
+ test_space_in_file_fun_RETURN=1
+ return 0
fi
if [[ ! -f $1 ]]; then
echo -e "\n### test_space_in_file_fun ERROR ### $1 FILE NOT PRESENT IN `dirname $1`\n"
- return 1
+ test_space_in_file_fun_RETURN=1
+ return 0
fi
# main code
local TEMPO_SPACE_COUNT=$(grep -o ' ' $1 | wc -l)
if [[ $TEMPO_SPACE_COUNT == 0 ]] ; then
echo -e "\ntest_space_in_file_fun MESSAGE: NO SPACE DETECTED IN $1\n"
- return 2
+ test_space_in_file_fun_RETURN=2
+ return 0
else
echo -e "\ntest_space_in_file_fun MESSAGE: ${TEMPO_SPACE_COUNT} SPACES DETECTED IN $1\n"
+ test_space_in_file_fun_RETURN=0
return 0
fi
}
@@ -133,6 +145,8 @@ function test_space_in_file_fun () {
function space_replacement_in_file_fun () {
# DESCRIPTION
# replace each block of succesive spaces by a single character string (default: _._) and save in -o (by default $1_replace)
+ # WARNING
+ # I had to use a global variable file_pattern_detection_fun_RETURN and not a local one to be able to deal with the check.sh file in genetic_linkage project
# ARGUMENTS
# $0: name of the function
# -i or --input: file name and path
@@ -140,9 +154,9 @@ function space_replacement_in_file_fun () {
# IF -o not specified, the file name is -i_replace and must not already exists in -i location
# -r or --replace: character string replacement (default "_._" if not specified)
# RETURN OUTPUT
- # 0: -i saved in -o then spaces replaced in -o
- # 1: error in options
- # 2: no space detected
+ # space_replacement_in_file_fun_RETURN=0: -i saved in -o then spaces replaced in -o
+ # space_replacement_in_file_fun_RETURN=1: error in options
+ # space_replacement_in_file_fun_RETURN=2: no space detected
# EXAMPLES
# space_replacement_in_file_fun -i /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/freq
# space_replacement_in_file_fun -i /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/Group1.txt
@@ -170,17 +184,20 @@ function space_replacement_in_file_fun () {
if [[ -z $INPUT_FUN ]]; then
echo -e "\n### space_replacement_in_file_fun ERROR ### OPTION -i REQUIRED\n"
- return 1
+ space_replacement_in_file_fun_RETURN=1
+ return 0
elif [[ ! -f $INPUT_FUN ]]; then
echo -e "\n### space_replacement_in_file_fun ERROR ### ${INPUT_FUN} FILE NOT PRESENT IN `dirname $INPUT_FUN`\n"
- return 1
+ space_replacement_in_file_fun_RETURN=1
+ return 0
fi
if [[ -z $OUTPUT_FUN ]]; then
local OUTPUT_FUN=${INPUT_FUN}_replace
fi
if [[ -f $OUTPUT_FUN ]]; then
echo -e "\n### space_replacement_in_file_fun ERROR ### ${OUTPUT_FUN} FILE ALREADY EXISTS\n"
- return 1
+ space_replacement_in_file_fun_RETURN=1
+ return 0
fi
if [[ -z $REPLACE_FUN ]]; then
local REPLACE_FUN="_._"
@@ -189,11 +206,13 @@ function space_replacement_in_file_fun () {
local TEMPO_SPACE_COUNT=$(grep -o ' \+' $INPUT_FUN | wc -l) # \ \+ from 1 to n spaces. Beware: \ * is from 0 to n
if [[ $TEMPO_SPACE_COUNT == 0 ]] ; then
echo -e "\nspace_replacement_in_file_fun MESSAGE: NO SPACE REPLACED SINCE NO SPACE DETECTED IN ${INPUT_FUN}\n"
- return 2
+ space_replacement_in_file_fun_RETURN=2
+ return 0
else
echo -e "\nspace_replacement_in_file_fun MESSAGE: ${INPUT_FUN} SAVED IN ${OUTPUT_FUN} AND ${TEMPO_SPACE_COUNT} SPACES REPLACED BY ${REPLACE_FUN} IN ${OUTPUT_FUN}\n"
cat $INPUT_FUN > $OUTPUT_FUN # save the initial file
sed -i "s/\ \+/$REPLACE_FUN/g" $OUTPUT_FUN # space replacement by _._ in file
+ space_replacement_in_file_fun_RETURN=0
return 0
fi
}
@@ -203,6 +222,8 @@ function space_replacement_in_file_fun () {
function file_pattern_detection_fun () {
# DESCRIPTION
# identify the lines of a file that contain a pattern
+ # WARNING
+ # I had to use a global variable file_pattern_detection_fun_RETURN and not a local one to be able to deal with the check.sh file in genetic_linkage project
# ARGUMENTS
# $0: name of the function
# -i or --input: file name and path
@@ -214,9 +235,9 @@ function file_pattern_detection_fun () {
# IF -c not specified, the file name is -i_wo_pattern and must not already exists at -i location
# -d or --detect: pattern (default "^#" if not specified, meaning detection of lines starting by #). Any regex between quotes
# RETURN OUTPUT
- # 0: at least one line contains the pattern -> saved in -o
- # 1: error in options
- # 2: no pattern detected
+ # file_pattern_detection_fun_RETURN=0: at least one line contains the pattern -> saved in -o
+ # file_pattern_detection_fun_RETURN=1: error in options
+ # file_pattern_detection_fun_RETURN=2: no pattern detected
# EXAMPLES
# file_pattern_detection_fun -i /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/pedfile1.pro -d "^#|^$" # line starting by #or empty line
# argument checking
@@ -225,7 +246,7 @@ function file_pattern_detection_fun () {
((OPTIND--)) # or ((OPTIND-1)) ?
fi
}
- local OPTIND OPTION i o c d INPUT_FUN OUTPUT_FUN OUTPUT_WOPATTERN_FUN CHARACTER_FUN
+ local OPTIND OPTION i o c d INPUT_FUN OUTPUT_FUN OUTPUT_WOPATTERN_FUN CHARACTER_FUN RETURN
while getopts ":i:o:c:d:" OPTION ; do
# add : after the option name to specify that something is required (-h has nothing required after)
# the first : before h is to induce getopts switching to "silent error reporting mode" (disable annoying messages).
@@ -234,32 +255,36 @@ function file_pattern_detection_fun () {
o) verif $OPTARG ; OUTPUT_FUN=$OPTARG ;;
c) verif $OPTARG ; OUTPUT_WOPATTERN_FUN=$OPTARG ;;
d) verif $OPTARG ; CHARACTER_FUN=$OPTARG ;;
- \?) echo -e "\n### file_pattern_detection_fun ERROR ### INVALID OPTION\n" ; return 1 ;;
- :) echo -e "\n### file_pattern_detection_fun ERROR ### OPTION -${OPTARG} REQUIRES AN ARGUMENT\n" ; return 1 ;;
+ \?) echo -e "\n### file_pattern_detection_fun ERROR ### INVALID OPTION\n" ; RETURN=1 ; return 0 ;;
+ :) echo -e "\n### file_pattern_detection_fun ERROR ### OPTION -${OPTARG} REQUIRES AN ARGUMENT\n" ; RETURN=1 ; return 0 ;;
esac
done
shift $((OPTIND-1))
if [[ -z $INPUT_FUN ]]; then
echo -e "\n### file_pattern_detection_fun ERROR ### OPTION -i REQUIRED\n"
- return 1
+ file_pattern_detection_fun_RETURN=1
+ return 0
elif [[ ! -f $INPUT_FUN ]]; then
echo -e "\n### file_pattern_detection_fun ERROR ### ${INPUT_FUN} FILE NOT PRESENT IN `dirname $INPUT_FUN`\n"
- return 1
+ file_pattern_detection_fun_RETURN=1
+ return 0
fi
if [[ -z $OUTPUT_FUN ]]; then
local OUTPUT_FUN=${INPUT_FUN}_pattern
fi
if [[ -f $OUTPUT_FUN ]]; then
echo -e "\n### file_pattern_detection_fun ERROR ### ${OUTPUT_FUN} FILE ALREADY EXISTS\n"
- return 1
+ file_pattern_detection_fun_RETURN=1
+ return 0
fi
if [[ -z $OUTPUT_WOPATTERN_FUN ]]; then
local OUTPUT_WOPATTERN_FUN=${INPUT_FUN}_wo_pattern
fi
if [[ -f $OUTPUT_WOPATTERN_FUN ]]; then
echo -e "\n### file_pattern_detection_fun ERROR ### ${OUTPUT_WOPATTERN_FUN} FILE ALREADY EXISTS\n"
- return 1
+ file_pattern_detection_fun_RETURN=1
+ return 0
fi
if [[ -z $CHARACTER_FUN ]]; then
local CHARACTER_FUN="^#"
@@ -272,9 +297,11 @@ function file_pattern_detection_fun () {
rm $OUTPUT_FUN
rm $OUTPUT_WOPATTERN_FUN
echo -e "\nfile_pattern_detection_fun MESSAGE: NO $CHARACTER_FUN PATTERN DETECTED IN $INPUT_FUN\n"
- return 2
+ file_pattern_detection_fun_RETURN=2
+ return 0
else
echo -e "\nfile_pattern_detection_fun MESSAGE: PATTERN $CHARACTER_FUN DETECTED IN $INPUT_FUN\n"
+ file_pattern_detection_fun_RETURN=0
return 0
fi
}
@@ -284,10 +311,12 @@ function file_pattern_detection_fun () {
function test_column_nb_perline_in_file_fun () {
# DESCRIPTION
# test if the number of column is identical for each line of a file
+ # WARNING
+ # I had to use a global variable file_pattern_detection_fun_RETURN and not a local one to be able to deal with the check.sh file in genetic_linkage project
# ARGUMENTS
# $0: name of the function
# -i or --input: file name and path. Must be tab delimited
- # -o or --output: output file in which problematic lines are printed.
+ # -o or --output: output file in which problematic lines are printed (lines with different number of columns than non empty first line).
# If -o specified, the file must not exists.
# IF -o not specified, by default, the file name is -i_error_line and must not already exists at -i location
# -c or --cleanoutput: output file containing the lines without the problematic lines.
@@ -295,11 +324,11 @@ function test_column_nb_perline_in_file_fun () {
# IF -c not specified, the file name is -i_wo_error_line and must not already exists at -i location
# -d or --detect: file separator pattern to count the number of columns (default "\t" if not specified). Any regex between quotes
# RETURN OUTPUT
- # 0: no difference in column number for each line of -i
- # 1: error in options
- # 2: error: empty first line
- # 3: only the first line has a different column number from the rest of the $1 file
- # 4: error lines (difference in column number in -i lines compared to 1st line of -i) -> printed in -o. First column is line number of -i. No error lines printed in -c
+ # test_column_nb_perline_in_file_fun_RETURN=0: no difference in column number for each line of -i
+ # test_column_nb_perline_in_file_fun_RETURN=1: error in options
+ # test_column_nb_perline_in_file_fun_RETURN=2: error: empty first line
+ # test_column_nb_perline_in_file_fun_RETURN=3: only the first line has a different column number from the rest of the $1 file
+ # test_column_nb_perline_in_file_fun_RETURN=4: error lines (difference in column number in -i lines compared to 1st line of -i) -> printed in -o. First column is line number of -i. No error lines printed in -c
# EXAMPLE
# test_column_nb_perline_in_file_fun -i /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/freq
# test_column_nb_perline_in_file_fun -i /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume/Group1/pedfile1.pro_wo_pattern
@@ -326,24 +355,28 @@ function test_column_nb_perline_in_file_fun () {
if [[ -z $INPUT_FUN ]]; then
echo -e "\n### test_column_nb_perline_in_file_fun ERROR ### OPTION -i REQUIRED\n"
- return 1
+ test_column_nb_perline_in_file_fun_RETURN=1
+ return 0
elif [[ ! -f $INPUT_FUN ]]; then
echo -e "\n### test_column_nb_perline_in_file_fun ERROR ### ${INPUT_FUN} FILE NOT PRESENT IN `dirname $INPUT_FUN`\n"
- return 1
+ test_column_nb_perline_in_file_fun_RETURN=1
+ return 0
fi
if [[ -z $OUTPUT_ERROR_FUN ]]; then
local OUTPUT_ERROR_FUN=${INPUT_FUN}_error_line
fi
if [[ -f $OUTPUT_ERROR_FUN ]]; then
echo -e "\n### test_column_nb_perline_in_file_fun ERROR ### ${OUTPUT_ERROR_FUN} FILE ALREADY EXISTS\n"
- return 1
+ test_column_nb_perline_in_file_fun_RETURN=1
+ return 0
fi
if [[ -z $OUTPUT_WO_ERROR_FUN ]]; then
local OUTPUT_WO_ERROR_FUN=${INPUT_FUN}_wo_error_line
fi
if [[ -f $OUTPUT_WO_ERROR_FUN ]]; then
echo -e "\n### test_column_nb_perline_in_file_fun ERROR ### ${OUTPUT_WO_ERROR_FUN} FILE ALREADY EXISTS\n"
- return 1
+ test_column_nb_perline_in_file_fun_RETURN=1
+ return 0
fi
if [[ -z $CHARACTER_FUN ]]; then
local CHARACTER_FUN="\t"
@@ -362,7 +395,8 @@ function test_column_nb_perline_in_file_fun () {
# echo -e "NB_COL_FIRSTLINE: $NB_COL_FIRSTLINE\n"
if [[ -z $NB_COL_FIRSTLINE || $NB_COL_FIRSTLINE == 0 ]] ; then
echo -e "\n### test_column_nb_perline_in_file_fun ERROR ### THE FIRST LINE OF $INPUT_FUN IS EMPTY: USE file_pattern_detection_fun TO REMOVE EMPTY LINES\n"
- return 2
+ test_column_nb_perline_in_file_fun_RETURN=2
+ return 0
fi
awk -F "$CHARACTER_FUN" -v var1=$NB_COL_FIRSTLINE 'NF!=var1{print NR, $0}' $INPUT_FUN > ${OUTPUT_ERROR_FUN} # recover the error lines
awk -F "$CHARACTER_FUN" -v var1=$NB_COL_FIRSTLINE 'NF==var1{print $0}' $INPUT_FUN > $OUTPUT_WO_ERROR_FUN
@@ -372,12 +406,14 @@ function test_column_nb_perline_in_file_fun () {
echo -e "\ntest_column_nb_perline_in_file_fun MESSAGE: NO DIFFERENT COLUMN NUMBER FOUND IN LINES OF ${INPUT_FUN} HAVING $NB_COL_FIRSTLINE COLUMNS IN THE FIRST LINE\n"
rm ${OUTPUT_ERROR_FUN}
rm ${OUTPUT_WO_ERROR_FUN}
+ test_column_nb_perline_in_file_fun_RETURN=0
return 0
elif [[ $NB_ERROR_LINES == $(( ${TOTAL_NB_LINES} - 1 )) ]]; then
echo -e "\ntest_column_nb_perline_in_file_fun MESSAGE: ONLY THE FIRST LINE HAS A DIFFERENT COLUMN NUMBER FROM THE REST OF THE ${INPUT_FUN} FILE\nTHE FIRST LINE IS:\n$(head -n 1 $INPUT_FUN)"
rm ${OUTPUT_ERROR_FUN}
rm ${OUTPUT_WO_ERROR_FUN}
- return 3
+ test_column_nb_perline_in_file_fun_RETURN=3
+ return 0
else
echo -e "test_column_nb_perline_in_file_fun MESSAGE: ${NB_ERROR_LINES} LINES FOUND IN ${INPUT_FUN} SHOWING A NUMBER OF COLUMN DIFFERENT FROM $NB_COL_FIRSTLINE COLUMNS AS FOUND IN THE FIRST LINE\n" # | tee -a $OUTPUT_ERROR_FUN
# echo -e "THE PROBLEMATIC LINES ARE:\n" >> $OUTPUT_ERROR_FUN
@@ -388,36 +424,40 @@ function test_column_nb_perline_in_file_fun () {
else
echo -e "\ntest_column_nb_perline_in_file_fun MESSAGE: THE PROBLEMATIC LINES ARE MORE THAN 200 -> ONLY PRINTED IN THE $OUTPUT_ERROR_FUN FILE:\n"
fi
- return 4
+ test_column_nb_perline_in_file_fun_RETURN=4
+ return 0
fi
}
function single_path_with_regex_fun { # comes from little_bash_functions-v1.0.0/little_bash_functions-v1.0.0.sh
# DESCRIPTION
# check that $1 path exists and is single
- # BEWARE
+ # WARNING
# do not use set -e !
+ # I had to use a global variable file_pattern_detection_fun_RETURN and not a local one to be able to deal with the check.sh file in genetic_linkage project
# ARGUMENTS
# $0: name of the function
# $1: first argument, ie path with regex
# RETURN OUTPUT
- # 0: single path detected is valid
- # 1: error: $1 not provided
- # 2: error: $2 provided or more than one path detected
- # 3: single url detected does not exist
- # 4: single path detected does not exist
+ # single_path_with_regex_fun_RETURN=0: single path detected is valid
+ # single_path_with_regex_fun_RETURN=1: error: $1 not provided
+ # single_path_with_regex_fun_RETURN=2: error: $2 provided or more than one path detected
+ # single_path_with_regex_fun_RETURN=3: single url detected does not exist
+ # single_path_with_regex_fun_RETURN=4: single path detected does not exist
# EXAMPLES
# single_path_with_regex_fun /cygdrive/c/Users/Gael/Desktop/config_tars_lodscore_gael_2017121[[:digit:]].conf
# single_path_with_regex_fun /pasteur/homes/gmillot/dyslexia/code_gael/config_tars_lodscore_gael_2017121[[:digit:]].conf
# argument checking
if [[ -z $1 ]] ; then
echo -e "\n### ERROR ### ARGUMENT 1 REQUIRED IN single_path_with_regex_fun\n"
- return 1
+ single_path_with_regex_fun_RETURN=1
+ return 0
fi
# main code
if [[ ! -z $2 ]] ; then
echo -e "\n### ERROR ###\n1) AT LEAST ARGUMENT 2 PRESENT IN single_path_with_regex_fun WHILE ONLY ONE REQUIRED OR\n2) REGEX PATH RESULT IN SEVERAL RESULTS:\n$@\n"
- return 2
+ single_path_with_regex_fun_RETURN=2
+ return 0
fi
local ARG1="$1"
# echo $ARG1 # print ARG1
@@ -427,21 +467,25 @@ function single_path_with_regex_fun { # comes from little_bash_functions-v1.0.0/
# echo "LENGTH: $ARG1_ARR_LENGTH" # print the length of the array
if [[ $ARG1_ARR_LENGTH != 0 ]] ; then
echo -e "\n### ERROR ### SPECIFIED REGEXP PATH IN single_path_with_regex_fun CORRESPOND TO MORE THAN ONE PATH: ${ARG1_ARR_LENGTH[@]}\n";
- return 2
+ single_path_with_regex_fun_RETURN=2
+ return 0
else
shopt -s extglob # -s unable global extention, ie the recognition of special global pattern in path, like [[:digit:]]
if [[ $(echo ${ARG1_ARR[0]} | grep -cE '^http' ) == 1 ]] ; then # -cE to specify extended and -c to return the number of match (here 0 or one only)
if [[ $(wget ${ARG1_ARR[0]} >/dev/null 2>&1 ; echo $?) != 0 ]] ; then # check the valid url. wget $url >/dev/null 2>&1 prevent any action and print. echo $? print the result of the last command (0 = success, other number = failure)
echo -e "\n### ERROR ### SPECIFIED URL IN single_path_with_regex_fun DOES NOT EXISTS: ${ARG1_ARR[0]}\n";
shopt -u extglob # -u disable global extention, ie the recognition of special global pattern in path, like [[:digit:]]
- return 3
+ single_path_with_regex_fun_RETURN=3
+ return 0
fi
elif [[ ! ( -d ${ARG1_ARR[0]} || -f ${ARG1_ARR[0]} ) ]] ; then
echo -e "\n### ERROR ### SPECIFIED PATH IN single_path_with_regex_fun DOES NOT EXISTS: ${ARG1_ARR[0]}\n";
shopt -u extglob # -u disable global extention, ie the recognition of special global pattern in path, like [[:digit:]]
- return 4
+ single_path_with_regex_fun_RETURN=4
+ return 0
else
shopt -u extglob # -u disable global extention, ie the recognition of special global pattern in path, like [[:digit:]]
+ single_path_with_regex_fun_RETURN=0
return 0
fi
fi
@@ -452,30 +496,35 @@ function var_existence_check_fun {
# check that $1 variable exists
# $0: name of the function
# $1: first argument, ie variable name without $
- # BEWARE
+ # WARNING
# do not use set -e !
+ # I had to use a global variable file_pattern_detection_fun_RETURN and not a local one to be able to deal with the check.sh file in genetic_linkage project
# RETURN OUTPUT
- # 0: variable is detected in the environment
- # 1: error: $1 not provided
- # 2: error: $2 provided or more than one path detected
- # 3: variable does not exist
+ # var_existence_check_fun_RETURN=0: variable is detected in the environment
+ # var_existence_check_fun_RETURN=1: error: $1 not provided
+ # var_existence_check_fun_RETURN=2: error: $2 provided or more than one path detected
+ # var_existence_check_fun_RETURN=3: variable does not exist
# EXAMPLES
#
# argument checking
if [[ -z $1 ]] ; then
echo -e "\n### ERROR ### ARGUMENT 1 REQUIRED IN var_existence_check_fun\n"
- return 1
+ var_existence_check_fun_RETURN=1
+ return 0
fi
# main code
if [[ ! -z $2 ]] ; then
echo -e "\n### ERROR ###\n1) AT LEAST ARGUMENT 2 PRESENT IN var_existence_check_fun WHILE ONLY ONE REQUIRED OR\n2) REGEX PATH RESULT IN SEVERAL RESULTS:\n$@\n"
- return 2
+ var_existence_check_fun_RETURN=2
+ return 0
fi
ARG1=$(echo $1)
ARG2=$(echo ${!ARG1}) # double because I need to know if the content of $(echo $1) is "" (echo return "" when does not exist)
if [[ -z "$ARG2" ]] ; then # test if $ARG1 is ""
- return 3
+ var_existence_check_fun_RETURN=3
+ return 0
else
+ var_existence_check_fun_RETURN=0
return 0
fi
}
@@ -485,14 +534,16 @@ function file_exten_verif_name_recov_fun () {
# DESCRIPTION
# check the file extension and recover the name of the file without extension
# See https://www.gnu.org/software/bash/manual/html_node/Shell-Parameter-Expansion.html
+ # WARNING
+ # I had to use a global variable file_pattern_detection_fun_RETURN and not a local one to be able to deal with the check.sh file in genetic_linkage project
# ARGUMENTS
# $0: name of the function
# -i or --input: file name, with or without the path
# -e or --extensionpattern: character string of the extension, including dot (default ".txt" if not specified). Example: .txt
# RETURN OUTPUT
- # 0: pattern detected and name of the file without the extension printed
- # 1: error in options
- # 2: extension pattern not detected at the end of the file name
+ # file_exten_verif_name_recov_fun_RETURN=0: pattern detected and name of the file without the extension printed
+ # file_exten_verif_name_recov_fun_RETURN=1: error in options
+ # file_exten_verif_name_recov_fun_RETURN=2: extension pattern not detected at the end of the file name
# EXAMPLES
# file_exten_verif_name_recov_fun -i /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume_split_initial_data/Famille1/pedfile.pro -e ".pro"
# VAR1=$(file_exten_verif_name_recov_fun -i /cygdrive/c/Users/Gael/Desktop/Archive_Guillaume_split_initial_data/Famille1/pedfile.pro -e ".pro") ; echo $VAR1
@@ -517,7 +568,8 @@ function file_exten_verif_name_recov_fun () {
if [[ -z $INPUT_FUN ]]; then
echo -e "\n### file_exten_verif_name_recov_fun ERROR ### OPTION -i REQUIRED\n"
- return 1
+ file_exten_verif_name_recov_fun_RETURN=1
+ return 0
fi
if [[ -z $PATTERN_FUN ]]; then
local PATTERN_FUN=".txt"
@@ -528,10 +580,12 @@ function file_exten_verif_name_recov_fun () {
local PATTERN_FUN_NCHAR=$(echo ${#PATTERN_FUN}) # recover the number of character of PATTERN_FUN
if [[ ${FILENAME: -$PATTERN_FUN_NCHAR} != ${PATTERN_FUN} ]] ; then
echo -e "\nfile_exten_verif_name_recov_fun MESSAGE: NO $PATTERN_FUN EXTENSION PATTERN DETECTED AT THE END OF $INPUT_FUN\n"
- return 2
+ file_exten_verif_name_recov_fun_RETURN=2
+ return 0
else
# do not write this because print output is assigned to a variable echo -e "\nfile_exten_verif_name_recov_fun MESSAGE: $PATTERN_FUN EXTENSION PATTERN CORRECTLY DETECTED AT THE END OF $INPUT_FUN\n"
echo ${FILENAME%${PATTERN_FUN}}
+ file_exten_verif_name_recov_fun_RETURN=0
return 0
fi
}
\ No newline at end of file