bash - Replacing strings in one file with strings from second file -

i've been searching couple of days haven't got right answer

i have 2 files this:

file1:

>contig-100_23331 length_200 read_count_4043  tcag... >contig-100_23332 length_200 read_count_4508  ttca... >contig-100_23333 length_200 read_count_184  ttcc... 

file2:

>contig-100_23331_cov:_30.9135 >contig-100_23332_cov:_125.591 >contig-100_23333_cov:_5.97537 

i want replace lines names (>contig... length...) in file1 lines names in file2. note file2 contains contig names (no sequence).

i suppose theres way sed, can't find solution

thanks in advance!

one possibility use sed create sed-script file2 used on file1:

sed 's/^\(>contig-[0-9]*_[0-9]*\)_.*/s%^\1 %& %/' file2 > sed.script sed -f sed.script file1 > file.out rm -f sed.script 

for sample file2, sed.script contain:

s%^>contig-100_23331 %>contig-100_23331_cov:_30.9135 % s%^>contig-100_23332 %>contig-100_23332_cov:_125.591 % s%^>contig-100_23333 %>contig-100_23333_cov:_5.97537 % 

for sample file1, output of sed processing be:

>contig-100_23331_cov:_30.9135 length_200 read_count_4043  tcag... >contig-100_23332_cov:_125.591 length_200 read_count_4508  ttca... >contig-100_23333_cov:_5.97537 length_200 read_count_184  ttcc... 

some versions of sed may have problems 23k lines in sed script. if that's problem you, can generate sed.script , split (split) smaller chunks (e.g. 1000 lines each) , run sed -f chunk each of chunks. that's painful, necessary. historically, hp-ux (archaic versions, hp-ux 9 or 10) had rather limited versions of sed handle few hundred commands in sed script.

given you're using bash, can avoid explicit intermediate file process substitution:

sed -f <(sed 's/^\(>contig-[0-9]*_[0-9]*\)_.*/s%^\1 %& %/' file2) file1 > file.out 

however, should validate script before using notation.