I have a quite large fixed format file without spaces (file1):
file1:
0808563800555550000367120000500000
0005555566369330000078020000500000
01066666780000000008933600009000005635
0904251263088000000786590056500000
0000469011009904440425120444444440
I want to extract lines with fields 4-8,11-15 and 20-24 when fields 4-8 (only) are in a list of IDs in file2
file2:
55555
42512
The desired outputs are:
55555 36933 07802
42512 08800 78659
I have tried the following combination of cut | grep commands:
cut -c 4-8,11-15,20-24 file1 --output-delimiter=' ' | grep -w -F -f file2
It works fine and the speed is very good, but the problem is that I am getting columns where the lookup ID (fields 4-8) is not in the first column of the cutted data, and that is because grep checks the three columns after cut, not only the first one.
Here are the outputs of the command above:
85638 55555 36712
55555 36933 07802
66666 00000 89336
42512 08800 78659
04690 00990 42512
I know one may write the output to a file and then use, for example awk, but I thought there could be a much simpler approach to avoid longer processing time (for example, makes grep picks only the match in a specific cutted column).
Any help will be very appreciated and many thanks!
With GNU awk for FIELDWIDTHS:
$ awk -v FIELDWIDTHS='3 5 2 5 4 5 *' 'NR==FNR{a[$0]; next} $2 in a{ print $2, $4, $6 }' file2 file1
55555 36933 07802
42512 08800 78659
Would you please try the following:
cut -c 4-8,11-15,20-24 file1 --output-delimiter=' ' | grep -wf <(sed 's/^/^/' file2)
Each line in file2 is prepended by a caret ^ character to anchor to
the start of the line of the output by cut.
It may be a bit slower than before due to the lack of -F option.
I have a fasta file with multiple headers:
>CABITT030000001.1 genome assembly, contig: 1, whole genome shotgun sequence
>CABITT030000002.1 genome assembly, contig: 2, whole genome shotgun sequence
.
.
.
.
And I would like to leave only the 1 and 2 either from the CABITT03000000*.1 or the number after the contig: string.
Output:
>1
>2
I was trying it with sed command, but it doesnt work.
sed 's/>.*/>1/' fasta.fa > newfasta.fa
Going on the example input you provided, this should work:
sed -e 's/.* contig: \([[:digit:]]\).*/>\1/' fasta.fa
>1
>2
Using a character class for the digit ([[:digit:]]), and capture groups (\( \) and reference that group with \1 in the replacement).
I have two lists, one of which contains wildcards (in this case represented by *). I would like to compare the two lists and create an output of those that match, with each wildcard * representing a single character.
For example:
File 1
123456|Jane|Johnson|Pharmacist|janejohnson#gmail.com
09876579|Frank|Roberts|Butcher|frankie1#hotmail.com
092362936|Joe|Jordan|Joiner|joe#joesjoinery.com
928|Bob|Horton|Farmer|bhorton#farmernews.co.uk
File 2
1***6|Jane|Johnson|Pharmacist|janejohnson#gmail.com
09876579|Frank|Roberts|Butcher|f**1#hotmail.com
092362936|Joe|Jordan|J*****|joe#joesjoinery.com
928|Bob|Horton|Farmer|b*****n#f*********.co.uk
Output
092362936|Joe|Jordan|Joiner|joe#joesjoinery.com
928|Bob|Horton|Farmer|bhorton#farmernews.co.uk
Explanation
The first two lines are not considered matches because the number of *s is not equal to the number of characters shown in the first file. The latter two are, so they are added to output.
I have tried to reason out ways to do this in AWK and using Join, but I don't know any way to even start trying to achieve this. Any help would be greatly appreciated.
$ cat tst.awk
NR==FNR {
file1[$0]
next
}
{
# Make every non-* char literal (see https://stackoverflow.com/a/29613573/1745001):
gsub(/[^^*]/,"[&]") # Convert every char X to [X] except ^ and *
gsub(/\^/,"\\^") # Convert every ^ to \^
# Convert every * to .:
gsub(/\*/,".")
# Add line start/end anchors
$0 = "^" $0 "$"
# See if the current file2 line matches any line from file1
# and if so print that line from file1:
for ( line in file1 ) {
if ( line ~ $0 ) {
print line
}
}
}
$ awk -f tst.awk file1 file2
092362936|Joe|Jordan|Joiner|joe#joesjoinery.com
928|Bob|Horton|Farmer|bhorton#farmernews.co.uk
sed 's/\./\\./g; s/\*/./g' file2 | xargs -I{} grep {} file1
Explanation:
I'd take advantage of regular expression matching. To do that, we need to turn every asterisk * into a dot ., which represents any character in regular expressions. As a side effect of enabling regular expressions, we need to escape all special characters, particularly the ., in order for them to be taken literally. In a regular expression, we need to use \. to represent a dot (as opposed to any character).
The first step is perform these substitutions with sed, the second is passing every resulting line as a search pattern to grep, and search file1 for that pattern. The glue that allows to do this is xargs, where a {} is a placeholder representing a single line from the results of the sed command.
Note:
This is not a general, safe solution you can simply copy and paste: you should watch out for any characters, in your file containing the asterisks, that are considered special in grep regular expressions.
Update:
jhnc extends the escaping to any of the following characters: .\^$[], thus accounting for almost all sorts of email addresses. He/she then avoids the use of xargs by employing -f - to pass the results of sed as search expressions to grep:
sed 's/[.\\^$[]/\\&/g; s/[*]/./g' file2 | grep -f - file1
This solution is both more general and more efficient, see comment below.
how to use grep to find occurrences of words from a dictionary file which have a given set of letters with the restriction that each letter occurs once and only once.
EG if the letters are abc then the expected output is:
cab
EDIT:
Given a dictionary file (that is a file containing one word per line such as /usr/share/dict/words on mac os x operating system) and a set of (unique) characters, I want to print out all of the dictionary file's words that contain each character of the input set once and only once. For example if the set of characters is {a,b,c} then print out all (3-letter) words that contain each character of the set.
I am looking, preferably, for a solution that uses just grep expressions.
Given a series of letters, for example abc, you can convert each one to a lookahead, like this:
^(?=[^a]*a[^a]*)(?=[^b]*b[^b]*)(?=[^c]*c[^c]*)$
You may need to use the "extended regex" flag -E to use this regex with grep.
To create this regex from a string, you could use sed (an exercise for the reader)
grep -E ^[abc]{3}.$ <Dictionary file> | grep -v -e a.*a -e b.*b -e c.*c
i.e. Find all three letter strings matching the input and pipe these through inverse grep to remove strings with double letters.
I'm using the '.' after {3} because my dictionary file is windows based so has an extra carriage return or line feed. So, that's probably not necessary.
Below is a Perl solution. Note, you'll need to add more words to the dictionary, and read input in to the $input variable. An array of valid words will end up in #results.
#!/usr/bin/env perl
use Data::Dumper;
my $input = "abc";
my #dictionary = qw(aaa aac aad aal aam aap aar aas aat aaw aba abc abd abf abg
abh abm abn abo abr abs abv abw aca acc ace aci ack acl acp acs act acv ada adb
adc add adf adh adl adn ado adp adq adr ads adt adw aea aeb aec aed aef aes aev
afb afc afe aff afg afi afk afl afn afp aft afu afv agb agc agl agm agn ago agp
...
PUT A REAL DICTIONARY HERE!
...
zie zif zig zii zij zik zil zim zin zio zip zir zis zit ziu ziv zlm zlo zlx zma
zme zmi zmu zna zoa zob zoe zog zoi zol zom zon zoo zor zos zot zou zov zoy zrn
zsr zub zud zug zui zuk zul zum zun zuo zur zus zut zuz zva zwo zye zzz);
# Generate a lookahead expression for each character in the input word
my $regexp = join("", map { "(?=.*$_)" } split(//, $input));
my #results;
foreach my $word (#dictionary) {
# If the size of the input doesn't match the dictionary word, skip to the
# next word.
if (length($input) != length($word)) {
next;
}
if ($word =~ /$regexp/) {
push(#results, $word);
}
}
print Dumper #results;
The solution I found involves using grep first to extract all n-letter words that contain only letters from the input set - although some letters might appear more than once, some may not appear; (again I am assuming that the input letters are unique). Then it does a series of 1-letter greps to make sure each letter occurs at least once. Because the words are of length n this ensures the word contains each letter once and only once. For example, if the input character set is (a,b,c} then the solution would be:
grep -E '^[abc]{3}$' /usr/share/dict/words | grep a | grep b | grep c
a simple bash script can be written which creates this grep string and executes it against the word file, using $1 as the input letter set. It might not be the most efficient method of generating the string, but as I am not familiar with sed or awk it does seem to solve my problem. The script I created is:
#!/bin/sh
slen=${#1}
g2="'^[$1]{$slen}\$'"
g3=""
ix1=0
while [ $ix1 -lt $slen ]
do
g3="$g3 | grep ${1:$ix1:1}"
ix1=$((ix1+1))
done
eval grep -E $g2 /usr/share/dict/words $g3
How do I remove or address a specific occurrence of a character in sed?
I'm editing a CSV file and I want to remove all text between the third and the fifth occurrence of the comma (that is, dropping fields four and five) . Is there any way to achieve this using sed?
E.g:
% cat myfile
one,two,three,dropthis,dropthat,six,...
% sed -i 's/someregex//' myfile
% cat myfile
one,two,three,,six,...
If it is okay to consider cut command then:
$ cut -d, -f1-3,6- file
awk or any other tools that are able to split strings on delimiters are better for the job than sed
$ cat file
1,2,3,4,5,6,7,8,9,10
Ruby(1.9+)
$ ruby -ne 's=$_.split(","); s[2,3]=nil ;puts s.compact.join(",") ' file
1,2,6,7,8,9,10
using awk
$ awk 'BEGIN{FS=OFS=","}{$3=$4=$5="";}{gsub(/,,*/,",")}1' file
1,2,6,7,8,9,10
A real parser in action
#!/usr/bin/python
import csv
import sys
cr = csv.reader(open('my-data.csv', 'rb'))
cw = csv.writer(open('stripped-data.csv', 'wb'))
for row in cr:
cw.writerow(row[0:3] + row[5:])
But do note the preface to the csv module:
The so-called CSV (Comma Separated
Values) format is the most common
import and export format for
spreadsheets and databases. There is
no “CSV standard”, so the format is
operationally defined by the many
applications which read and write it.
The lack of a standard means that
subtle differences often exist in the
data produced and consumed by
different applications. These
differences can make it annoying to
process CSV files from multiple
sources. Still, while the delimiters
and quoting characters vary, the
overall format is similar enough that
it is possible to write a single
module which can efficiently
manipulate such data, hiding the
details of reading and writing the
data from the programmer.
$ cat my-data.csv
1
1,2
1,2,3
1,2,3,4,
1,2,3,4,5
1,2,3,4,5,6
1,2,3,4,5,6,
1,2,,4,5,6
1,2,"3,3",4,5,6
1,"2,2",3,4,5,6
,,3,4,5
,,,4,5
,,,,5
$ python csvdrop.py
$ cat stripped-data.csv
1
1,2
1,2,3
1,2,3
1,2,3
1,2,3,6
1,2,3,6,
1,2,,6
1,2,"3,3",6
1,"2,2",3,6
,,3
,,
,,