[SOLVED] Removing lines which match with specific pattern from another file

Issue

I've got two files (I only show the beginning of these files) :

patterns.txt

m64071_201130_104452/13
m64071_201130_104452/26
m64071_201130_104452/46
m64071_201130_104452/49
m64071_201130_104452/113
m64071_201130_104452/147

myfile.txt

>m64071_201130_104452/13/ccs
ACAGTCGAGCG
>m64071_201130_104452/16/ccs
ACAGTCGAGCG
>m64071_201130_104452/20/ccs
CAGTCGAGCGC
>m64071_201130_104452/22/ccs
CACACATCTCG
>m64071_201130_104452/26/ccs
TAGACAATGTA

I should get an output like that :

>m64071_201130_104452/13/ccs
ACAGTCGAGCG
>m64071_201130_104452/26/ccs
TAGACAATGTA

I want to create a new file if the lines in patterns.txt match with the lines in myfile.txt . I need to keep the letters ACTG associated with the pattern in question. I use :

for i in $(cat patterns.txt); do 
     grep -A 1 $i myfile.txt; done > my_newfile.txt

It works, but it's very slow to create the new file... The files I work on are pretty large but not too much (14M for patterns.txt and 700M for myfile.txt).

I also tried to use grep -v because I have the another file which contains the others patterns of myfile.txt not present in patterns.txt. But it is the same "speed filling file" problem.

If you see a solution..

Solution

Another awk:

$ awk -F/ '                            # / delimiter
NR==FNR {
    a[$1,$2]                           # hash patterns to a
    next
}
{
    if( tf=((substr($1,2),$2) in a) )  # if first part found in hash
        print                          # output and store found result in var tf
    if(getline && tf)                  # read next record and if previous record was found
        print                          # output
}' patterns myfile

Output:

>m64071_201130_104452/13/ccs
ACAGTCGAGCG
>m64071_201130_104452/26/ccs
TAGACAATGTA

Edit: To output the ones not found:

$ awk -F/ '                              # / delimiter
NR==FNR {
    a[$1,$2]                             # hash patterns to a
    next
}
{
    if( tf=((substr($1,2),$2) in a) ) {  # if first part found in hash
        getline                          # consume the next record too
        next
    }
    print                                # otherwise output
}' patterns myfile

Output:

>m64071_201130_104452/16/ccs
ACAGTCGAGCG
>m64071_201130_104452/20/ccs
CAGTCGAGCGC
>m64071_201130_104452/22/ccs
CACACATCTCG

Answered By - James Brown