Replace ids from file1 with that of file2 - awk

I have two text files and I want to replace id from file1 with that of file2. All the ids are in the same order in both the files.
File1
>12_abc
ghfghfjgfhjgfjf
hgfjfgjgfjfgjgfjf
>13_def
ghfghgfgfgfghfjhf
nmbnmbhjgkjgjhggh
>14_ghi
uytghhuytuytuytuyt
ytrftyfrghfhgfgfgg
File2
>12_abc|10
>13_def|20
>14_ghi|30
Desired Output
>12_abc|10
ghfghfjgfhjgfjf
hgfjfgjgfjfgjgfjf
>13_def|20
ghfghgfgfgfghfjhf
nmbnmbhjgkjgjhggh
>14_ghi|30
uytghhuytuytuytuyt
ytrftyfrghfhgfgfgg
awk '{print} !(NR%2) {if ((getline < "File2.txt") > -1) print}' File1


This looks awkwardly a lot as a FASTA file. This is how I would do it:
If you want to replace the name in order:
awk '(NR==FNR){a[FNR]=$0;next}/^>/{print a[++c]; next}1' File2 File1 > File1.new
If you want to replace the name based on the content:
awk -F '|' '(NR==FNR){a[$1]=$0;next}/^>/{print a[$0]; next}1' File2 File1 > File1.new

Related

Retrieve all rows from 2 columns matching from 2 different files

I need to retrieve all rows from a file starting from some column matching from another file.
My first file is:
col1,col2,col3
1TF4,WP_110462952.1,AEV67733.1
1TF4,EGD45884.1,AEV67733.1
2BTO,NP_006073.2,XP_037953971.1
2BTO,XP_037953971.1,XP_037953971.1
The second one is:
col1,col2,col3,col4,col5
BAA13425.1,SDD02770.1,38.176,296,175
BAA13425.1,WP_002465021.1,32.056,287,185
BBE42932.1,AEG17356.1,40.909,110,64
BBE42932.1,WP_048124638.1,40.367,109,64
I want to retrieve all rows from the second file, where its file2_col1=file1_col3 and file2_col2=file1_col1
I tried like this but it doesn't print everything
awk -F"," 'FILENAME=="file1"{A[$3$2]=$3$2}
FILENAME=="file2"{if(A[$1$2]){print $0}}' file1 file2 > test

I want to retrieve all rows from the second file, where its file2_col1=file1_col3 and file2_col2=file1_col1
You may use this 2 pass awk solution:
awk -F, 'FNR == NR {seen[$3,$1]; next} FNR == 1 || ($1,$2) in seen' file1 file2
col1,col2,col3,col4,col5
BAA13425.1,2BTO,32.056,287,185
BAA13425.1,2BTO,12.410,641,123
Where input files are:
cat file1
col1,col2,col3
1TF4,WP_110462952.1,AEV67733.1
1TF4,EGD45884.BAA13425.1
2BTO,NP_006073.2,BAA13425.1
2BTO,XP_037953971.1,BAA13425.1
cat file2
col1,col2,col3,col4,col5
BAA13425.1,SDD02770.1,38.176,296,175
BAA13425.1,2BTO,32.056,287,185
BBE42932.1,AEG17356.1,40.909,110,64
BBE42932.1,WP_048124638.1,40.367,109,64
BAA13425.1,2BTO,12.410,641,123

Filter column matches from two files

I have two files with the format:
number|string
I want to create a third file with the contents of file 1 and without the matches between both files on the second column.
file1
1|abc
2|bcd
3|cde
file2
1|bcd
2|def
file3
1|abc
3|cde
Is this correct?
awk -F '|' 'NR==FNR{a[$2];next}$2 not in a{print $0}' file1 file2 > file3

You may use this awk:
awk -F '|' 'FNR == NR {skip[$2]; next} !($2 in skip)' file2 file1 > file3
cat file3
1|abc
3|cde

Match values in two files and replace values in specific columns

The purpose is to check if values for column 2 and 3 in file1 match with column 1 in file2. If any value match, then replace values in file2 for column 2 and 3 using the information of file1 columns 4 and 5.
file1
100,31431,37131,999991.70,2334362.30
100,31431,37471,111113.20,2334363.30
100,31433,36769,777775.60,2334361.90
102,31433,36853,333322.00,2334362.80
file2
3143137113 318512.50 2334387.50 100
3143137131 318737.50 2334387.50 100
3143137201 319612.50 2334387.50 100
3143137219 319837.50 2334387.50 100
3143137471 322987.50 2334387.50 100
3143137491 323237.50 2334387.50 100
3143336687 313187.50 2334412.50 100
3143336723 313637.50 2334412.50 100
3143336769 314212.50 2334412.50 100
3143336825 314912.50 2334412.50 100
3143336853 315262.50 2334412.50 102
Output desired
31431,37113,318512.50,2334387.50,100
31431,37131,999991.70,2334362.30,100
31431,37201,319612.50,2334387.50,100
31431,37219,319837.50,2334387.50,100
31431,37471,111113.20,2334363.30,100
31431,37491,323237.50,2334387.50,100
31433,36687,313187.50,2334412.50,100
31433,36723,313637.50,2334412.50,100
31433,36769,777775.60,2334361.90,100
31433,36825,314912.50,2334412.50,100
31433,36853,333322.00,2334362.80,102
I tried
awk -F[, ] 'FNR==NR{a[$1 $2]=$0;next}$1 in a{print $0 ,a[$1 $2]}' file1 file2
Thanks in advance

Could you please try following.
awk '
BEGIN{
OFS=","
}
FNR==NR{
a[$2 $3]=$2 OFS $3
b[$2 $3]=$4;c[$2 $3]=$5
next
}
($1 in a){
$2=b[$1]
$3=c[$1];$1=a[$1]
print
next
}
{
$1=$1
sub(/^...../,"&,",$1)
print
}
' FS="," file1 FS=" " file2
Output will be as follows.
31431,37113,318512.50,2334387.50,100
31431,37131,999991.70,2334362.30,100
31431,37201,319612.50,2334387.50,100
31431,37219,319837.50,2334387.50,100
31431,37471,111113.20,2334363.30,100
31431,37491,323237.50,2334387.50,100
31433,36687,313187.50,2334412.50,100
31433,36723,313637.50,2334412.50,100
31433,36769,777775.60,2334361.90,100
31433,36825,314912.50,2334412.50,100
31433,36853,333322.00,2334362.80,102

Try this:
$ awk -F, 'NR==FNR{tmp=$0;sub($1 FS,"",tmp);a[$2 $3]=tmp;next} $1 in a{print a[$1],$NF;next} {$1=substr($1,1,5) OFS substr($1,6,5);} 1' OFS=, file1 FS=' ' file2
31431,37113,318512.50,2334387.50,100
31431,37131,999991.70,2334362.30,100
31431,37201,319612.50,2334387.50,100
31431,37219,319837.50,2334387.50,100
31431,37471,111113.20,2334363.30,100
31431,37491,323237.50,2334387.50,100
31433,36687,313187.50,2334412.50,100
31433,36723,313637.50,2334412.50,100
31433,36769,777775.60,2334361.90,100
31433,36825,314912.50,2334412.50,100
31433,36853,333322.00,2334362.80,102
Above assumes $1 of file does not include regex characters, so to be accurate and safe, better use this:
awk -F, 'NR==FNR{$1="";a[$2 $3]=substr($0,2);next} $1 in a{print a[$1],$NF;next} {$1=substr($1,1,5) OFS substr($1,6,5);} 1' OFS=, file1 FS=' ' file2
However this one assumes the FS of file1 is 1 character only.
And that leads to another change/efficiency improvement:
awk -F, 'NR==FNR{a[$2 $3]=substr($0,length($1 FS)+1);next} $1 in a{print a[$1],$NF;next} {$1=substr($1,1,5) OFS substr($1,6,5);} 1' OFS=, file1 FS=' ' file2

Print default value if index is not in awk array

$ cat file1 #It contains ID:Name
5:John
4:Michel
$ cat file2 #It contains ID
5
4
3
I want to Replace the IDs in file2 with Names from file1, output required
John
Michel
NO MATCH FOUND
I need to expand the below code to reult NO MATCH FOUND text.
awk -F":" 'NR==FNR {a[$1]=$2;next} {print a[$1]}' file1 file2
My current result:
John
Michel
<< empty line
Thanks,

You can use a ternary operator for this: print ($1 in a)?a[$1]:"NO MATCH FOUND". That is, if $1 is in the array, print it; otherwise, print the text "NO MATCH FOUND".
All together:
$ awk -F":" 'NR==FNR {a[$1]=$2;next} {print ($1 in a)?a[$1]:"NO MATCH FOUND"}' f1 f2
John
Michel
NO MATCH FOUND

You can test whether the index occurs in the array:
$ awk -F":" 'NR==FNR {a[$1]=$2;next} $1 in a {print a[$1]; next} {print "NOT FOUND"}' file1 file2
John
Michel
NOT FOUND

if file2 has only digit (no space at the end)
awk -F ':' '$1 in A {print A[$1];next}{if($2~/^$/) print "NOT FOUND";else A[$1]=$2}' file1
if not
awk -F '[:[:blank:]]' '$1 in A {print A[$1];next}{if($2~/^$/) print "NOT FOUND";else A[$1]=$2}' file1 file2

output the record by comparing string in other file using awk script

I want to output the record having matching string in another file using awk script
file1 code
849002|48|1208004|1
849007|28|1208004|1
855003|48|1208004|1
855004|28|1208004|1
855006|28|1208004|1
file2 code :
00990029000000004804470425|ST1400029|0.550|Recurring|1248073|ST1400029
00990029000000008410517183|IM1450029|1.000|Recurring|855003|ST1400029
009900290000000000007800612988|IM3350029|1.000|Recurring|1248063|ST1400029
Notice that 855003 occurs in the middle row of each sample? That's the match I'm looking for, and the output should be:
00990029000000008410517183|IM1450029|1.000|Recurring|855003|ST1400029
Because I want to search $1 of file1 in $5 in file2, if match found then output the line
I tried this but its returning zero record
awk 'NR==FNR{a[$1]=$1;next}a[$5]{print $0}' file2 file1 > outfile
Your help will resolve my issue, I have to search long list of data

Don't forget to set the delimiter using the -F flag:
awk -F "|" 'FNR==NR { a[$1]; next } $5 in a' file1 file2
Results:
00990029000000008410517183|IM1450029|1.000|Recurring|855003|ST1400029

try this (didn't test)
awk 'NR==FNR{a[$1];next}$5 in a' file1 file2