then, elif, else statement that I have programmed in a bash script. I know that it works because I can run the same command in the terminal interface and see that it is doing what I want it to do. However when I run it in a script it seems to always jump to the else statement and not detect anything. Can anybody help explain why this is so? Here is my script code:
if [ -e "$1" ]
then
for line in `samtools view -H $1`
do
if [[ "$line" == *NCBI-Build-36\.1* ]]
then
echo "hg18"
break
elif [[ "$line" == *hg19* ]]
then
echo "hg19"
break
else
echo "Reference was not found, manual entry required: "
read ans
echo "$ans"
break
fi
done
else
echo -e "Usage: \e[1;32mreadRef.sh \e[1;36mbamfile.bam"
fi
No matter what file I plug in it always skips to the else and asks me for manual entry.
Here is the command I ran on terminal:
for line in `samtools view -H $bignormal`; do if [[ "$line" == *NCBI-Build-36\.1* ]]; then echo "YES - $line"; else echo "NO - $line"; fi; done
And the output is like this:
NO - #HD
NO - VN:1.0
NO - GO:none
NO - SO:coordinate
NO - #SQ
NO - SN:1
NO - LN:247249719
YES - AS:NCBI-Build-36.1
YES - UR:http://www.bcgsc.ca/downloads/genomes/9606/NCBI-Build-36.1/bwa_ind/genome/
NO - SP:Homo
NO - sapiens
.
.
.
Why is the script not detecting the string I am looking for, but it is in terminal?
EDIT:
I tried what Charles said, this is the output:
:+'[' -e /projects/rcorbettprj2/DLBCL/CNV/RG065/normal/A01440_8_lanes_dupsFlagged.bam ']'
::+samtools view -H /projects/rcorbettprj2/DLBCL/CNV/RG065/normal/A01440_8_lanes_dupsFlagged.bam
:+for line in '`samtools view -H $1`'
:+case "$line" in
:+echo 'Reference was not found, manual entry required: '
Reference was not found, manual entry required:
:+read ans
I think your code has a logic error nobody's spotted yet. I'm not sure, since you haven't told us what the script's supposed to be doing, but it looks to me like what you want is to ask for manual entry only if you don't find a match to either of your patterns anywhere in the output, but what you're actually doing is examining only the first word of output for a match. And from your sample output, the first word is "#HD", which doesn't match either pattern, so the script is doing exactly what I'd expect.
Now, assuming I'm right and that the point is to look for either pattern anywhere in the output, you can actually simplify things a bit. Mainly, you don't need the loop, you can just do a single comparison to look for the pattern in the entire output at once:
#!/bin/bash
if [ -e "$1" ]
then
output="$(samtools view -H "$1")"
if [[ "$output" == *NCBI-Build-36.1* ]]
then
echo "hg18"
elif [[ "$output" == *hg19* ]]
then
echo "hg19"
else
read -p "Reference was not found, manual entry required: " ans
echo "$ans"
fi
done
else
echo -e "Usage: \e[1;32mreadRef.sh \e[1;36mbamfile.bam"
fi
Related
Made a script that the user gives a "parameter" and it prints out if it is a file, directory or non of them. This is it :
#!/bin/bash
read parametros
for filename in *
do
if [ -f "$parametros" ];
then
echo "$parametros is a file"
elif [ -d "$parametros" ];
then
echo "$parametros is a directory"
else
echo " There is not such file or directory"
fi
exit
done
Altough i want the user to be allowed to give only one word as a parameter. How do i make this happen ? (For example if user press space after first word there would be an error message showing "wrong input")
#!/bin/bash
read parametros
if [[ "$parametros" = *[[:space:]]* ]]
then
echo "wrong input"
elif [[ -f "$parametros" ]]
then
echo "$parametros is a file"
elif [[ -d "$parametros" ]]
then
echo "$parametros is a directory"
else
echo " There is not such file or directory"
fi
See http://mywiki.wooledge.org/BashFAQ/031 for the difference between [...] and [[...]].
You have to use the $#. It gives the number of the parameters.
The code will be something like:
if [ "$#" -ne 1 ]; then
printf 'ERROR!\n'
exit 1
fi
First, I'm curious why you want to restrict to one word - a file or directory could have spaces in it, but maybe you are preventing that somehow in your context.
Here are a few ways you could approach it:
Validate the input after they enter it - check if it has any spaces, eg: if [[ "parametros" == *" " ]]; then...
Get one character at a time in a while loop, eg with: read -n1 char
Show an error if it's a space
Break the loop if it's 'enter'
Build up the overall string from the entered characters
1 is obviously much simpler, but maybe 2 is worth the effort for the instant feedback that you are hoping for?
I wrote this shell code, but it doesn't get the good output.
Even though the $csoport gets the "...: No such user" output, id doesn't echoes the following line I wrote there.
read felhasznalo
while [ "$felhasznalo" != "exit" ]
do
csoport=`groups $felhasznalo`
echo "$csoport"
if [[ "$csoport" == *": No such user"* ]] ; then
echo -n "Nincs ilyen felhasznalo a rendszerben"
else
echo "$csoport"
fi
echo -n "Felhasznalo: "
read felhasznalo
done
You shouldn't try to match the error messsage since you only care if groups fails. You ought to do:
if ! csoport=$(groups "$felhasznalo"); then
printf "Nincs ilyen felhasznalo a rendszerben"
else
echo "$csoport"
fi
i stumbled in a confusing way of conditionally returning value based on variable. I would like to check if process is successful then echo "process success", but if it's failed, i want to check specific error message then return the error message,
ERRMSG="$(cd /nonexist 2>&1)"
if [ $? -ne 0 ]
then
if [ -z "$ERRMSG|grep -o 'No such file or directory'|head -1" ]
then
echo "empty" >> $FQLOGNAME
else
echo $ERRMSG|grep -o 'No such file or directory'|head -1 >> $FQLOGNAME
fi
else
echo "success" >> $FQLOGNAME
fi
Please advice,
Thanks
You don't need to use grep to check if a string contains a substring. The built-in pattern matching in Bash is sufficient. This code should do something close to what you want:
if ERRMSG=$(cd /nonexist 2>&1) ; then
echo 'process success'
elif [[ $ERRMSG == *'No such file or directory'* ]] ; then
echo 'No such file or directory'
else
echo 'empty'
fi >> "$FQLOGNAME"
See the Conditional Constructs section of the Bash Reference Manual for details of the pattern matching capabilities of [[...]].
I've retained the ERRMSG and FQLOGNAME variables, but note that it's best to avoid ALL_UPPERCASE variable names. There is a danger that they will clash with environment variables or Bash builtin variables. See Correct Bash and shell script variable capitalization.
To find error messages defined by a pattern in multi-line error messages, and only print the first one, you can use regular expression matching (=~) in [[...]]. To provide a concrete example, this code assumes that error messages consist of 'ERROR' followed by one or more spaces followed by a decimal number:
# Example function for testing
function dostuff
{
printf 'Output line A\n'
printf 'Encountered ERROR 29\n' >&2
printf 'Output line B\n'
printf 'Encountered ERROR 105\n' >&2
printf 'Output line C\n'
return 1
}
# Regular expression matching an error string
readonly error_rx='ERROR +[0-9]+'
if ERRMSG=$(dostuff 2>&1) ; then
echo 'process success'
elif [[ $ERRMSG =~ $error_rx ]] ; then
printf '%s\n' "${BASH_REMATCH[0]}"
else
echo 'empty'
fi >> "$FQLOGNAME"
It appends 'ERROR 29' to the log file.
For more information about Bash's built-in regular expression matching see mklement0's answer to "How do I use a regex in a shell script?".
Make it simpler and easier:
if ! ERRMSG=$(cd /nonexist 2>&1); then
if <<<"$ERRMSG" grep -q 'No such file or directory'; then
# if the error string contains the message 'No such file or directory'
echo "empty" >> "$FQLOGNAME"
else
printf "Unhandled cd error: %s" "$ERRMSG" >> "$FQLOGNAME"
fi
else
echo "process success" >> "$FQLOGNAME"
fi
if statements checks for the return status of a COMMAND. [ or test is just a command, which return a status. The return status of assignment is the same as command status. What I mean, is that out=$(cmd); if [ "$?" -eq 0 ]; then is the same as if out=$(cmd); then.
Using HERE-strings is a bit better than echo "$string". Echo is not that much portable, better get used to printf "%s" "$string" which is a portable way. However HERE-strings puts additional EOF at the end of the stream, which sometimes breaks while read loops, but for most cases works ok.
Don't if [ -z "$(echo smth | grep ..)" ]; then. You can just check grep return status, just if echo smth | grep ...; then or with HERE-strings if <<<"smth" grep -q ...; then or if grep -q ... file; then. The -q option which has --quiet or --silent alternatives makes grep produce no output.
The quoting is not needed when assigning a variable from a single command substitution. tmp="$(...)" is just the same as tmp=$(...).
Say you have the user enter in a number 0-3 and want to test it. The most common way seems to be:
[[ $var =~ ^[0-3]$ ]]
But how would you use this with:
test expression
My initial attempt doesn't evaluate correctly, e.g.
read -p "Enter selection [0-3] > "
if test $REPLY == '^[0-3]$' ; then
...
It just evaluates the if statement as false.
test is equivalent to the [ ] structure, but not to [[ ]], which is an extended version. The regex =~ is only available in the extended test, so for simple test or [ ] you have to pull the regex evaluation from elsewhere.
One fix is grep. This pipeline will catch and print the matches:
echo "$REPLY" | grep '^[0-3]$'
Using test with a string evaluates positively if the string is non-empty. Compare these two:
test "" && echo ok
and
test "a" && echo ok
Knowing this, it's now easy to build a compound test from the both elements.
test "$(echo "$REPLY" | grep '^[0-3]$')"
And this can be applied to the script:
read -p "Enter selection [0-3] > "
if test "$(echo "$REPLY" | grep '^[0-3]$')"; then
...
fi
You can use a regex in Bash like this:
echo -n "Your answer> "
read REPLY
if [[ $REPLY =~ ^[0-9]+$ ]]; then
echo Numeric
else
echo Non-numeric
fi
Please check the post Using Bash's regular expressions.
I want in a bash script (Linux) to check, if two files are identical.
I use the following code:
#!/bin/bash
…
…
differ=$(diff $FILENAME.out_ok $FILENAME.out)
echo "******************"
echo $differ
echo "******************"
if [ $differ=="" ]
then
echo "pass"
else
echo "Error ! different output"
echo $differ
fi
The problem:
the diff command return white space and break the if command
output
******************
82c82 < ---------------------- --- > ---------------------
******************
./test.sh: line 32: [: too many arguments
Error ! different output
The correct tool for checking whether two files are identical is cmp.
if cmp -s $FILENAME.out_ok $FILENAME.out
then : They are the same
else : They are different
fi
Or, in this context:
if cmp -s $FILENAME.out_ok $FILENAME.out
then
echo "pass"
else
echo "Error ! different output"
diff $FILENAME.out_ok $FILENAME.out
fi
If you want to use the diff program, then double quote your variable (and use spaces around the arguments to the [ command):
if [ -z "$differ" ]
then
echo "pass"
else
echo "Error ! different output"
echo "$differ"
fi
Note that you need to double quote the variable when you echo it to ensure that newlines etc are preserved in the output; if you don't, everything is mushed onto a single line.
Or use the [[ test:
if [[ "$differ" == "" ]]
then
echo "pass"
else
echo "Error ! different output"
echo "$differ"
fi
Here, the quotes are not strictly necessary around the variable in the condition, but old school shell scripters like me would put them there automatically and harmlessly. Roughly, if the variable might contain spaces and the spaces matter, it should be double quoted. I don't see a need to learn a special case for the [[ command when it works fine with double quotes too.
Instead of:
if [ $differ=="" ]
Use:
if [[ $differ == "" ]]
Better to use modern [[ and ]] instead of an external program /bin/[
Also use diff -b to compare 2 files while ignoring white spaces
#anubhava answer is correct,
you can also use
if [ "$differ" == "" ]