replace header in a file with list of lines in another file

Question

I have a fasta file contained ~28000 sequence. I want to replace header of these sequences by a list of lines in another file. Example:

File 1:

sp|B7UM99|TIR_ECO27
MPIGNLGNNVNGNHLIPPAPP.....
sp|P0ACF8|HNS_ECOLI
MSEALKILNNIRTLRAQ........
sp|P24232|HMP_ECOLI
MLDAQTIATVKATIPLLVET..........

File 2:

sp|B7UM99|TIR_ECO27OS=Escherichia coli
sp|P0ACF8|HNS_ECOLI=Human
sp|P24232|HMP_ECOLI=Flavohemoprotein

Desired Output:

sp|B7UM99|TIR_ECO27OS=Escherichia coli
MPIGNLGNNVNGNHLIPPAPP.....
sp|P0ACF8|HNS_ECOLI=Human
MSEALKILNNIRTLRAQ........
sp|P24232|HMP_ECOLI=Flavohemoprotein
MLDAQTIATVKATIPLLVET..........

Answer 1

Perhaps, the script below is what you need:

#!/bin/bash

# Save the good lines
awk '{if($0 !~ "^sp")print > "result_1" }' < file_1
awk '{if($0 ~ "^sp")print > "result_2" }' < file_2

# Get number of lines in result_1 ( == nl in result_2 )
nl_file=$(wc -l result_1|cut -d' ' -f1)

# Prepare sorting of these files preceded by a number
seq 2 2 $(( ${nl_file} * 2 )) > numbered_file_1
seq 1 2 $(( ${nl_file} * 2 )) > numbered_file_2

# paste content of numbered_file_* and result_* side by side
paste -d ' ' numbered_file_1 result_1 > mergedfiles
paste -d ' ' numbered_file_2 result_2 >> mergedfiles

sort -n mergedfiles | sed 's/^[[:digit:]]\s\+//g'

Answer 2

Assuming that all lines in file 2 begin with sp|, and that the sp| lines in file 1 don't contain any regexp characters that would confuse grep:

$ cat file.sh
while read line
do
        case "${line}" in
        sp\|*)
                grep "^$line" file2 || printf '%s\n' "$line"
        ;;
        *)
                printf '%s\n' "$line"
        esac
done
$ sh file.sh < file1
sp|B7UM99|TIR_ECO27OS=Escherichia coli
MPIGNLGNNVNGNHLIPPAPP.....
sp|P0ACF8|HNS_ECOLI=Human
MSEALKILNNIRTLRAQ........
sp|P24232|HMP_ECOLI=Flavohemoprotein
MLDAQTIATVKATIPLLVET..........

I would have liked to use the -F option to grep, but I felt that it was more important to require that the match be anchored to beginning-of-line.