Match a line and cat multiple files into one file

Question

I have a file with 3 columns and 4426 row some thing like this

file1 :

DAEQUEG00000025 FP3SLUG00002140 FOMPING00001058 
DAEQUEG00001923 FP3SLUG00002391 FOMPING00000186 
DAEQUEG00000047 FP3SLUG00002116 FOMPING00001081 
DAEQUEG00000321 FP3SLUG00006281 FOMPING00000374

and I have same number of files and named in same way (DAEQUEG00000025.fa FP3SLUG00002140.fa FOMPING00001058.fa)

I would like to match the first line to a list of files and cat them into one file.

expected output(first line in one file)

>DAEQUEG00000025  
ATGTTGTTTAGATTGGCCCGGCGAGCTACAAGCCCGCTCACCCGCTCGATGGCGACGCAT
GCGCGAGGACTCCCTGCTCTACTCGAGAAGAAACCAGACGATGTAGTCATAACATTCGCA
>FP3SLUG00002140
AAGCGTACTGCTATGGCACGCGCGAGGAAGGGTCAGCTAAAGGACATCCCTGTCGACGAG
>FOMPING00001058 
CTTATGCAGGCTCTCATCAAGACTCAGCTCGATCCAGCTATGCTAGAGGACATATGCGTA
GGGACTTGTCACCCTCCGTCACCGACGTACATCTCTCGAGCAGCTGCTCTTGCTGCTGGA

*4426 row* and *i have same number of files* means 4426 files? — RomanPerekhrest, Feb 14 '17 at 13:21
Just the first line? Then you want to cat a total of 3 files? — jas, Feb 14 '17 at 13:26
@RomanPerekhrest yes every row has 3 files put into one file — kapr0001, Feb 14 '17 at 14:07
@jas i havent tired but i did for few line which is time consuming, just sought of help — kapr0001, Feb 14 '17 at 14:09

score 0 · Answer 1 · answered Feb 14 '17 at 15:49

You can try,

while read -r a b c; do 
    cat "$a.fa" "$b.fa" "$c.fa" > "${a}_${b}_${c}.fa"; 
done < file1

you get several files with compound name as output, for example

DAEQUEG00000025_FP3SLUG00002140_FOMPING00001058.fa

>DAEQUEG00000025  
ATGTTGTTTAGATTGGCCCGGCGAGCTACAAGCCCGCTCACCCGCTCGATGGCGACGCAT
GCGCGAGGACTCCCTGCTCTACTCGAGAAGAAACCAGACGATGTAGTCATAACATTCGCA
>FP3SLUG00002140
AAGCGTACTGCTATGGCACGCGCGAGGAAGGGTCAGCTAAAGGACATCCCTGTCGACGAG
>FOMPING00001058 
CTTATGCAGGCTCTCATCAAGACTCAGCTCGATCCAGCTATGCTAGAGGACATATGCGTA
GGGACTTGTCACCCTCCGTCACCGACGTACATCTCTCGAGCAGCTGCTCTTGCTGCTGGA

Match a line and cat multiple files into one file

1 Answers1