print matching lines from file1 and file2

Question

I have a file1.txt and file2.txt i would like to print the matching lines to a new files

file1.txt

FOMPING00002015
FOMPING00008750 
FOMPING00003379 
FOMPING00009073
FOMPING00007164 
FOMPING00009598

file2.txt

>FOMPING00013293 Protein of unknown function
ATGCCCTGCTCGTCGCTCGAGCGGGATCATAGCCAGCATGAAGTTATACCGTCATCGCAG
AGCCAGGAACGCGACTTTGTGCCGCCTAATGGTGACATCAGGAGTCGGGCGAGAACGACA
TCCGACGAAATTGTACCCACATCGCAG
>FOMPING00003379 Protein of unknown function
ATGCCCTGCTCGTCGCTCGAGCGGGATCATAGCCAGCATGAAGTTATACCGTCATCGCAG
AGCCAGGAACGCGACTTTGTGCCGCCTAATGGTGACATCAGGAGTCGGGCGAGAACGACA
TCCGACGAAATTGTACCCACATCGCAGTA
>FOMPING00009073 Protein of unknown function 
ATGTCCTCTTGGTCTGGTTCTTCTTACCCTCCACCTCCACGCGCACGTTCGCGCTCTCGC
TCCCCTTATCGTGGGTCTTATCCTGCGAGACCCGGGTATCCAGAGCCTGGATACTCGCAG
>FOMPING00000581 Similar to mcs4: Response regulator mcs4  
ATGTCCTCTTGGTCTGGTTCTTCTTACCCTCCACCTCCACGCGCACGTTCGCGCTCTCGC
TCCCCTTATCGTGGGTCTTATCCTGCGAGACCCGGGTATCCAGAGCCTGGATACTCGCAG
GATCCATACCGTGCCGACTGGGAGGCTTATGACAGAGAGCGCGCATGGGCCTCCTACGAG

I have tried few commands

grep -F file1.txt file2.txt > output.txt
grep -Ff file1.txt file2.txt > output.txt

both the commands outputs just the first line from file2.txt

output.txt

>FOMPING00013293 Protein of unknown function
>FOMPING00000581 Similar to mcs4: Response regulator mcs4.

I want the output file just like the file2.txt with sequences in it.

Thank you

Answer 1

This seems to work ok in my tests. The trick is to use ">" as record / block separator.

awk 'NR==FNR{a[$0];next};$1 in a{print ">" $0}' file1.txt RS=">" file2.txt
#or alternativelly, due to the whitespace present in the end of each line of file1.txt
awk 'NR==FNR{a[$1];next};$1 in a{print ">" $0}' file1.txt RS=">" file2.txt

The position of RS in the end of awk, affects the file that comes after RS. In my command, file1 is parsed with default RS="\n" , but file2 is parsed with RS=">".

Answer 2

Using awk with two input field separators > and the space character:

awk -F'[> ]' '{
  if (NR==FNR){
    a[$1]
  }
  else {
    if (substr($0,0,1) == ">"){
      printline=($2 in a)
    }
    if (printline){
      print
    }
  }
}' file1.txt file2.txt

When the first file is processed, store the first field in an array.
When the second file is processed, test if the current line begins with > and set a flag printline testing if the second field is present in the array. Print the current line if the flag is set.