I often need to find a particular sequence in a fasta file and print it. For those who don't know, fasta is a text file format for biological sequences (DNA, proteins, etc.). It's pretty simple, you have a line with the sequence name preceded by a '>' and then all the lines following until the next '>' are the sequence itself. For example:
>sequence1
ACTGACTGACTGACTG
>sequence2
ACTGACTGACTGACTG
ACTGACTGACTGACTG
>sequence3
ACTGACTGACTGACTG
The way I'm currently getting the sequence I need is to use grep with -A, so I'll do
grep -A 10 sequence_name filename.fa
and then if I don't see the start of the next sequence in the file, I'll change the 10 to 20 and repeat until I'm sure I'm getting the whole sequence.
It seems like there should be a better way to do this. For example, can I ask it to print up until the next '>' character?
Using the > as the record separator:
awk -v seq="sequence2" -v RS='>' '$1 == seq {print RS $0}' file
>sequence2
ACTGACTGACTGACTG
ACTGACTGACTGACTG
Like this maybe:
awk '/>sequence1/{p++;print;next} /^>/{p=0} p' file
So, if the line starts with >sequence1, set a flag (p) to start printing, print this line and move to next. On subsequent lines, if the line starts with >, change p flag to stop printing. In general, print if the flag p is set.
Or, improving a little on your grep solution, use this to cut off the -A (after) context:
grep -A 999999 "sequence1" file | awk 'NR>1 && /^>/{exit} 1'
So, that prints up to 999999 lines after sequence1 and pipes them into awk. Awk then looks for a > at the start of any line after line 1, and exits if it finds one. Until then, the 1 causes awk to do its standard thing, which is print the current line.
Using sed only:
sed -n '/>sequence3/,/>/ p' | sed '${/>/d}'
$ perl -0076 -lane 'print join("\n",#F) if $F[0]=~/sequence2/' file
This question has excellent answers already. However, if you are dealing with FASTA records often, I would highly recommend Python's Biopython Module. It has many options and make life easier if you want to manipulate FASTA records. Here is how you can read and print the records:
from Bio import SeqIO
import textwrap
for seq_record in SeqIO.parse("input.fasta", "fasta"):
print(f'>{seq_record.id}\n{seq_record.seq}')
#If you want to wrap the record into multiline FASTA format
#You can use textwrap module
for seq_record in SeqIO.parse("input.fasta", "fasta"):
dna_sequence = str(seq_record.seq)
wrapped_dna_sequence = textwrap.fill(dna_sequence, width=8)
print(f'>{seq_record.id}\n{wrapped_dna_sequence}')
Related
I have a large file A (consisting of emails), one line for each mail. I also have another file B that contains another set of mails.
Which command would I use to remove all the addresses that appear in file B from the file A.
So, if file A contained:
A
B
C
and file B contained:
B
D
E
Then file A should be left with:
A
C
Now I know this is a question that might have been asked more often, but I only found one command online that gave me an error with a bad delimiter.
Any help would be much appreciated! Somebody will surely come up with a clever one-liner, but I'm not the shell expert.
If the files are sorted (they are in your example):
comm -23 file1 file2
-23 suppresses the lines that are in both files, or only in file 2. If the files are not sorted, pipe them through sort first...
See the man page here
grep -Fvxf <lines-to-remove> <all-lines>
works on non-sorted files (unlike comm)
maintains the order
is POSIX
Example:
cat <<EOF > A
b
1
a
0
01
b
1
EOF
cat <<EOF > B
0
1
EOF
grep -Fvxf B A
Output:
b
a
01
b
Explanation:
-F: use literal strings instead of the default BRE
-x: only consider matches that match the entire line
-v: print non-matching
-f file: take patterns from the given file
This method is slower on pre-sorted files than other methods, since it is more general. If speed matters as well, see: Fast way of finding lines in one file that are not in another?
Here's a quick bash automation for in-line operation:
remove-lines() (
remove_lines="$1"
all_lines="$2"
tmp_file="$(mktemp)"
grep -Fvxf "$remove_lines" "$all_lines" > "$tmp_file"
mv "$tmp_file" "$all_lines"
)
GitHub upstream.
usage:
remove-lines lines-to-remove remove-from-this-file
See also: https://unix.stackexchange.com/questions/28158/is-there-a-tool-to-get-the-lines-in-one-file-that-are-not-in-another
awk to the rescue!
This solution doesn't require sorted inputs. You have to provide fileB first.
awk 'NR==FNR{a[$0];next} !($0 in a)' fileB fileA
returns
A
C
How does it work?
NR==FNR{a[$0];next} idiom is for storing the first file in an associative array as keys for a later "contains" test.
NR==FNR is checking whether we're scanning the first file, where the global line counter (NR) equals to the current file line counter (FNR).
a[$0] adds the current line to the associative array as key, note that this behaves like a set, where there won't be any duplicate values (keys)
!($0 in a) we're now in the next file(s), in is a contains test, here it's checking whether current line is in the set we populated in the first step from the first file, ! negates the condition. What is missing here is the action, which by default is {print} and usually not written explicitly.
Note that this can now be used to remove blacklisted words.
$ awk '...' badwords allwords > goodwords
with a slight change it can clean multiple lists and create cleaned versions.
$ awk 'NR==FNR{a[$0];next} !($0 in a){print > FILENAME".clean"}' bad file1 file2 file3 ...
Another way to do the same thing (also requires sorted input):
join -v 1 fileA fileB
In Bash, if the files are not pre-sorted:
join -v 1 <(sort fileA) <(sort fileB)
You can do this unless your files are sorted
diff file-a file-b --new-line-format="" --old-line-format="%L" --unchanged-line-format="" > file-a
--new-line-format is for lines that are in file b but not in a
--old-.. is for lines that are in file a but not in b
--unchanged-.. is for lines that are in both.
%L makes it so the line is printed exactly.
man diff
for more details
This refinement of #karakfa's nice answer may be noticeably faster for very large files. As with that answer, neither file need be sorted, but speed is assured by virtue of awk's associative arrays. Only the lookup file is held in memory.
This formulation also allows for the possibility that only one particular field ($N) in the input file is to be used in the comparison.
# Print lines in the input unless the value in column $N
# appears in a lookup file, $LOOKUP;
# if $N is 0, then the entire line is used for comparison.
awk -v N=$N -v lookup="$LOOKUP" '
BEGIN { while ( getline < lookup ) { dictionary[$0]=$0 } }
!($N in dictionary) {print}'
(Another advantage of this approach is that it is easy to modify the comparison criterion, e.g. to trim leading and trailing white space.)
You can use Python:
python -c '
lines_to_remove = set()
with open("file B", "r") as f:
for line in f.readlines():
lines_to_remove.add(line.strip())
with open("file A", "r") as f:
for line in [line.strip() for line in f.readlines()]:
if line not in lines_to_remove:
print(line)
'
You can use -
diff fileA fileB | grep "^>" | cut -c3- > fileA
This will work for files that are not sorted as well.
Just to add to the Python answer to the user above, here is a faster solution:
python -c '
lines_to_remove = None
with open("partial file") as f:
lines_to_remove = {line.rstrip() for line in f.readlines()}
remaining_lines = None
with open("full file") as f:
remaining_lines = {line.rstrip() for line in f.readlines()} - lines_to_remove
with open("output file", "w") as f:
for line in remaining_lines:
f.write(line + "\n")
'
Raising the power of set subtraction.
To get the file after removing the lines which appears on another file
comm -23 <(sort bigFile.txt) <(sort smallfile.txt) > diff.txt
Here is a one liner that pipes the output of a website and removes the navigation elements using grep and lynx! you can replace lynx with cat FileA and unwanted-elements.txt with FileB.
lynx -dump -accept_all_cookies -nolist -width 1000 https://stackoverflow.com/ | grep -Fxvf unwanted-elements.txt
To remove common lines between two files you can use grep, comm or join command.
grep only works for small files. Use -v along with -f.
grep -vf file2 file1
This displays lines from file1 that do not match any line in file2.
comm is a utility command that works on lexically sorted files. It
takes two files as input and produces three text columns as output:
lines only in the first file; lines only in the second file; and lines
in both files. You can suppress printing of any column by using -1, -2
or -3 option accordingly.
comm -1 -3 file2 file1
This displays lines from file1 that do not match any line in file2.
Finally, there is join, a utility command that performs an equality
join on the specified files. Its -v option also allows to remove
common lines between two files.
join -v1 -v2 file1 file2
I have a file with three columns, which has pipe as a delimiter. Now some lines in the file can have a "," instead of "|", due to some error. I want to output all such erroneous rows.
You can also use grep, it is more complicated:
egrep "\|.*\|.*\|" input
echo No pipe
egrep "^[^\|]*$" input
echo One pipe
egrep "^[^\|]*\|[^\|\]*$" input
echo 3+ pipe
egrep "\|[^\|]*\|[^\|\]*\|" input
Before combining the greps, first introduce new variables
p (pipe) and n (no pipe)
p="\|"
n="[^\|]*"
echo "p=$p, n=$n"
echo No pipe
egrep "^$n$" input
echo One pipe
egrep "^$n$p$n$" input
echo 3+ pipe
egrep "$p$n$p$n$p" input
Now bring all together
egrep "^$n$|^$n$p$n$|$p$n$p$n$p" input
Edit: The comments and variable names were about "slashes", but they are pipes (with backslashes). That was a bit confusing.
To count the number of columns with awk you can use the NF variable:
$ cat file
ABC|12345|EAR
PQRST|123|TWOEYES
ssdf|fdas,sdfsf
$ awk -F\| 'NF!=3' file
ssdf|fdas,sdfsf
However, this does not seem to cover all the possible ways the data could be corrupted based on the various revisions of the question and the comments.
A better approach would be to define the exact format that the data must follow. For example, assuming that a line is "correct" if it is three columns, with the first and third letters only, and the second numeric, you could write the following script to match all non conforming lines:
awk -F\| '!(NF==3 && $1$3 ~ /^[a-zA-Z]+$/ && $2+0==$2)' file
Test (notice that only the second line (which is conforming) does not get printed):
$ cat file
A,BC|12345|EAR
PQRST|123|TWOEYES
ssdf|fdas,sdfsf
ABC|3983|MAKE,
sf dl lfsdklf |kldsamfklmadkfmask |mfkmadskfmdslafmka
ABC|abs|EWE
sdf|123|123
$ awk -F\| '!(NF==3&&$1$3~/^[a-zA-Z]+$/&&$2+0==$2)' file
A,BC|12345|EAR
ssdf|fdas,sdfsf
ABC|3983|MAKE,
sf dl lfsdklf |kldsamfklmadkfmask |mfkmadskfmdslafmka
ABC|abs|EWE
sdf|123|12
You can adapt the above command to your specific needs, based on what you think is a valid input. For example, if you wanted to also restrict the length of each line to 50 characters, you could do
awk -F\| '!(NF==3 && $1$3 ~ /^[a-zA-Z]+$/ && $2+0==$2 && length($0)<50)' file
I have 2 files, one contains this :
file1.txt
632121S0 126.78.202.250 1
131145S0 126.178.20.250 1
the other contain this : file2.txt
632121S0 126.78.202.250 OBS
131145S0 126.178.20.250 OBS
313359S2 126.137.37.250 OBS
I want to end up with a third file which contains :
632121S0 126.78.202.250 OBS
131145S0 126.178.20.250 OBS
Only the lines which start by the same string in both files. I can't remember how to do it. I tried several grep, egrep and find, i still cannot use it properly...
Can you help please ?
You can use this awk:
$ awk 'FNR==NR {a[$1]; next} $1 in a' f1 f2
632121S0 126.78.202.250 OBS
131145S0 126.178.20.250 OBS
It is based on the idea of two file processing, by looping through files as this:
first loop through first file, storing the first field in the array a.
then loop through second file, checking if its first field is in the array a. If that is true, the line is printed.
To do this with grep, you need to use a process substitution:
grep -f <(cut -d' ' -f1 file1.txt) file2.txt
grep -f uses a file as a list of patterns to search for within file2. In this case, instead of passing file1 unaltered, process substitution is used to output only the first column of the file.
If you have a lot of these lines, then the utility join would likely be useful.
join - join lines of two files on a common field
Here's a set of examples.
Given is a file with the following structure:
a 123
b 876234
c 56456
d 65765
a 9879
b 9361
c 6527
d 823468
So there are blocks of data (lines beginning with a,b,c,d and an empty line divides two blocks) and I'm looking for a pattern (e.g. 9361) inside this file. If this pattern is found inside I want to copy the whole block (line starting with a 9879 and ending with d 823468) and write it to another file.
This pattern can be found zero or more times inside a file. If there are more than one results each block should be written to the other file.
How would you do it?
You can do it with gawk.
gawk 'BEGIN {RS=""} /here goes your pattern/ { print $0}' INPUTFILE > OUTPUTFILE
This sets gawk's record separator to the empty line(s).
HTH
Assuming your data is in file.txt, this is a solution in perl.
perl -00 -ne "print if /9361/" file.txt
The result is on stdout.
-00 causes perl to read the file a paragraph at a time.
-n causes perl to read filename arguments one by one.
-e is to specify a perl command.
Ruby(1.8+)
ruby -00 -ne 'print if /9361/' file
I am trying to parse a CSV containing potentially 100k+ lines. Here is the criteria I have:
The index of the identifier
The identifier value
I would like to retrieve all lines in the CSV that have the given value in the given index (delimited by commas).
Any ideas, taking in special consideration for performance?
As an alternative to cut- or awk-based one-liners, you could use the specialized csvtool aka ocaml-csv:
$ csvtool -t ',' col "$index" - < csvfile | grep "$value"
According to the docs, it handles escaping, quoting, etc.
See this youtube video: BASH scripting lesson 10 working with CSV files
CSV file:
Bob Brown;Manager;16581;Main
Sally Seaforth;Director;4678;HOME
Bash script:
#!/bin/bash
OLDIFS=$IFS
IFS=";"
while read user job uid location
do
echo -e "$user \
======================\n\
Role :\t $job\n\
ID :\t $uid\n\
SITE :\t $location\n"
done < $1
IFS=$OLDIFS
Output:
Bob Brown ======================
Role : Manager
ID : 16581
SITE : Main
Sally Seaforth ======================
Role : Director
ID : 4678
SITE : HOME
First prototype using plain old grep and cut:
grep "${VALUE}" inputfile.csv | cut -d, -f"${INDEX}"
If that's fast enough and gives the proper output, you're done.
CSV isn't quite that simple. Depending on the limits of the data you have, you might have to worry about quoted values (which may contain commas and newlines) and escaping quotes.
So if your data are restricted enough can get away with simple comma-splitting fine, shell script can do that easily. If, on the other hand, you need to parse CSV ‘properly’, bash would not be my first choice. Instead I'd look at a higher-level scripting language, for example Python with a csv.reader.
In a CSV file, each field is separated by a comma. The problem is, a field itself might have an embedded comma:
Name,Phone
"Woo, John",425-555-1212
You really need a library package that offer robust CSV support instead of relying on using comma as a field separator. I know that scripting languages such as Python has such support. However, I am comfortable with the Tcl scripting language so that is what I use. Here is a simple Tcl script which does what you are asking for:
#!/usr/bin/env tclsh
package require csv
package require Tclx
# Parse the command line parameters
lassign $argv fileName columnNumber expectedValue
# Subtract 1 from columnNumber because Tcl's list index starts with a
# zero instead of a one
incr columnNumber -1
for_file line $fileName {
set columns [csv::split $line]
set columnValue [lindex $columns $columnNumber]
if {$columnValue == $expectedValue} {
puts $line
}
}
Save this script to a file called csv.tcl and invoke it as:
$ tclsh csv.tcl filename indexNumber expectedValue
Explanation
The script reads the CSV file line by line and store the line in the variable $line, then it split each line into a list of columns (variable $columns). Next, it picks out the specified column and assigned it to the $columnValue variable. If there is a match, print out the original line.
Using awk:
export INDEX=2
export VALUE=bar
awk -F, '$'$INDEX' ~ /^'$VALUE'$/ {print}' inputfile.csv
Edit: As per Dennis Williamson's excellent comment, this could be much more cleanly (and safely) written by defining awk variables using the -v switch:
awk -F, -v index=$INDEX -v value=$VALUE '$index == value {print}' inputfile.csv
Jeez...with variables, and everything, awk is almost a real programming language...
For situations where the data does not contain any special characters, the solution suggested by Nate Kohl and ghostdog74 is good.
If the data contains commas or newlines inside the fields, awk may not properly count the field numbers and you'll get incorrect results.
You can still use awk, with some help from a program I wrote called csvquote (available at https://github.com/dbro/csvquote):
csvquote inputfile.csv | awk -F, -v index=$INDEX -v value=$VALUE '$index == value {print}' | csvquote -u
This program finds special characters inside quoted fields, and temporarily replaces them with nonprinting characters which won't confuse awk. Then they get restored after awk is done.
index=1
value=2
awk -F"," -v i=$index -v v=$value '$(i)==v' file
I was looking for an elegant solution that support quoting and wouldn't require installing anything fancy on my VMware vMA appliance. Turns out this simple python script does the trick! (I named the script csv2tsv.py, since it converts CSV into tab-separated values - TSV)
#!/usr/bin/env python
import sys, csv
with sys.stdin as f:
reader = csv.reader(f)
for row in reader:
for col in row:
print col+'\t',
print
Tab-separated values can be split easily with the cut command (no delimiter needs to be specified, tab is the default). Here's a sample usage/output:
> esxcli -h $VI_HOST --formatter=csv network vswitch standard list |csv2tsv.py|cut -f12
Uplinks
vmnic4,vmnic0,
vmnic5,vmnic1,
vmnic6,vmnic2,
In my scripts I'm actually going to parse tsv output line by line and use read or cut to get the fields I need.
Parsing CSV with primitive text-processing tools will fail on many types of CSV input.
xsv is a lovely and fast tool for doing this properly. To search for all records that contain the string "foo" in the third column:
cat file.csv | xsv search -s 3 foo
A sed or awk solution would probably be shorter, but here's one for Perl:
perl -F/,/ -ane 'print if $F[<INDEX>] eq "<VALUE>"`
where <INDEX> is 0-based (0 for first column, 1 for 2nd column, etc.)
Awk (gawk) actually provides extensions, one of which being csv processing.
Assuming that extension is installed, you can use awk to show all lines where a specific csv field matches 123.
Assuming test.csv contains the following:
Name,Phone
"Woo, John",425-555-1212
"James T. Kirk",123
The following will print all lines where the Phone (aka the second field) is equal to 123:
gawk -l csv 'csvsplit($0,a) && a[2] == 123 {print $0}'
The output is:
"James T. Kirk",123
How does it work?
-l csv asks gawk to load the csv extension by looking for it in $AWKLIBPATH;
csvsplit($0, a) splits the current line, and stores each field into a new array named a
&& a[2] == 123 checks that the second field is 123
if both conditions are true, it { print $0 }, aka prints the full line as requested.