My bash script contains the following line:
echo $(echo "$STRING_VAR" | cut -d' ' -f 2) >> $FILE
Here we have two echo calls, but are they really necessary ?
I wrote them, because otherwise the bash would think the string in first place is a command.
Simply echo "$STRING_VAR" | cut -d' ' -f 2 >> $FILE does the same thing.
echo "$STRING_VAR" | cut -d' ' -f 2 >> $FILE
should be all you need
Also, bash has the handy "here-string" redirection mode: you don't need echo at all:
cut -d' ' -f2 <<< "$STRING_VAR" >> "$FILE"
Related
I'm extracting two md5sums by using this code:
md5sum test{1,2} | cut -d' ' -f1-2
I'm receiving two md5sums as in example below:
02eace9cb4b99519b49d50b3e44ecebc
d8e8fca2dc0f896fd7cb4cb0031ba249
Afterwards I'm not sure how to compare them. I have tried using the xargs:
md5sum test{1,2} | cut -d' ' -f1-2 | xargs bash -c '$0 == $1'
However, it tries to execute md5sum as a command
Any advice?
Try using a command subsitution instead
#!/bin/bash
echo 1 > file_a
echo 2 > file_b
echo 1 > file_c
file1=file_a
# try doing "file2=file_b" as well
file2=file_c
if [[ $(sha1sum $file1 | cut -d ' ' -f1-2) = $(sha1sum $file2 | cut -d ' ' -f1-2) ]]; then
echo same
else
echo different
fi
when i use
echo -n "$str" |sha224sum
it gets me the checksum ends with "-"
how to get the checksum without it ?
Thanks
Cut the first field:
$ echo -n "$str" | sha224sum | cut -d' ' -f1
23097d223405d8228642a477bda255b32aadbce4bda0b3f7e36c9da7
I have a script such as :
cat list_id.txt | while read line; do for ACC in $line;
do
echo -n "$ACC\t"
curl -s "link=fasta&retmode=xml" |\
grep TSeq_taxid |\
cut -d '>' -f 2 |\
cut -d '<' -f 1 |\
tr -d "\n"
echo
sleep 0.25
done
done
This script allows me from a list of ID in list_id.txt to get the corresponding names in a database in https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=${ACC}&rettype=fasta&retmode=xml
So from this script I get something like
CAA42669\t9913
V00181\t7154
AH002406\t538120
And what I would like is directly to print or echo this result in fiel call new_ids.txt, I tried echo >> new_ids.txt but the file is empty.
Thanks for your help.
A minimal refactoring of your script might look like
# Avoid useless use of cat
# Use read -r
# Don't use upper case for private variables
while read -r line; do
for acc in $line; do
echo -n "$acc\t"
# No backslash necessary after | character
curl -s "link=fasta&retmode=xml" |
# Probably use a proper XML parser for this
grep TSeq_taxid |
cut -d '>' -f 2 |
cut -d '<' -f 1 |
tr -d "\n"
echo
sleep 0.25
done
done <list_id.txt >new_ids.txt
This could probably still be simplified significantly, but without knowledge of what your input file looks like exactly, or what curl returns, this is somewhat speculative.
tr -s ' \t\n' '\n' <list_id.txt |
while read -r acc; do
curl -s "link=fasta&retmode=xml" |
awk -v acc="$acc" '/TSeq_taxid/ {
split($0, a, /[<>]/); print acc "\t" a[3] }'
sleep 0.25
done <list_id.txt >new_ids.txt
given: file: files.txt with:
sara.gap sara.gao
pe.gap pe.gao
I just want to use f=sara in my bash skript, because I need f later in the skript. so i tryed: get ffirst line,second argument,remove .gao and save in f
f=sed -ne '1p' files.txt |cut -d " " -f2 |sed 's/.gao//g'
But did not work, please help me ;(
You just need backticks:
f=`head -1 files.txt | cut -d " " -f2 | sed 's/.gao//g'`
I'd do
read f junk < files.txt
f=${f%*.gap}
oh, and for second argument:
read junk f junk < files.txt
f=${f%*.gao}
That's completely in bash :-)
Use Command Substitution if you want to use the output of a command to set a variable. The format is v=$(command). You can also use backticks e.g. v=`command`, but this has been superseded by the $(...) form.
Your command would be:
f=$(sed -ne '1p' files.txt |cut -d " " -f2 |sed 's/.gao//g')
echo $f
prints
sara
you mean this?
f="sed -ne '1p' files.txt |cut -d ' ' -f2 |sed 's/.gao//g'"
eval "$f"
with output:
sara
You can use awk as well
f=$(awk 'NR==1{gsub(/\.gao/,"",$2);print $2;exit}' file)
I'm trying to write a little script which will open a text file and give me an md5 hash for each line of text. For example I have a file with:
123
213
312
I want output to be:
ba1f2511fc30423bdbb183fe33f3dd0f
6f36dfd82a1b64f668d9957ad81199ff
390d29f732f024a4ebd58645781dfa5a
I'm trying to do this part in bash which will read each line:
#!/bin/bash
#read.file.line.by.line.sh
while read line
do
echo $line
done
later on I do:
$ more 123.txt | ./read.line.by.line.sh | md5sum | cut -d ' ' -f 1
but I'm missing something here, does not work :(
Maybe there is an easier way...
Almost there, try this:
while read -r line; do printf %s "$line" | md5sum | cut -f1 -d' '; done < 123.txt
Unless you also want to hash the newline character in every line you should use printf or echo -n instead of echo option.
In a script:
#! /bin/bash
cat "$#" | while read -r line; do
printf %s "$line" | md5sum | cut -f1 -d' '
done
The script can be called with multiple files as parameters.
You can just call md5sum directly in the script:
#!/bin/bash
#read.file.line.by.line.sh
while read line
do
echo $line | md5sum | awk '{print $1}'
done
That way the script spits out directly what you want: the md5 hash of each line.
this worked for me..
cat $file | while read line; do printf %s "$line" | tr -d '\r\n' | md5 >> hashes.csv; done