Print line and following text based on pattern matching

Question

I am trying to filter lines from a text file based on patterns in proceeding lines which keeping the pattern matched line. I also need to rename the pattern matched files

for example:

>text chr1    
AAA  
BBA  
AAA  
>additional text chr2  
ABA  
AAA  
CCC  
TTT  
>some text chr3  
TTT  
CCC  
TCT  
>no good text 1 3  
AAA  
CCC  
TCT  
>unimportant text 2 3 3  
ACC  
CCC  
TCT  

the command would print the lines containing "chr" and all following lines until a line beginning with ">" does not contain "chr":

>chr1  
AAA  
BBA  
AAA  
>chr2  
ABA  
AAA  
CCC  
TTT  
>chr3   
TTT  
CCC  
TCT  

Answer 1

I did it using awk, grep and sed. Assuming there aren't trailing whitespaces in the original file.

awk 'NR>1&&/>/{print ""}{printf " %s", $0}END{print ""}' file |grep chr|sed 's/^ //' |sed 's/^.*chr/>chr/' |awk 'BEGIN{OFS="\n";}{print $1,$2,$3,$4}'

first, group blocks starting lines with '>' and preceding each field with a whitesapce

 >text chr1 AAA BBA AAA
 >additional text chr2 ABA AAA CCC TTT
 >some text chr3 TTT CCC TCT
 >no good text 1 3 AAA CCC TCT
 >unimportant text 2 3 3 ACC CCC TCT

second, filter oll tthe lines that contain the substring "chr"

 >text chr1 AAA BBA AAA
 >additional text chr2 ABA AAA CCC TTT
 >some text chr3 TTT CCC TCT

third, remove all leading whitespace

>text chr1 AAA BBA AAA
>additional text chr2 ABA AAA CCC TTT
>some text chr3 TTT CCC TCT

fourth, remove all characters between ">" and "chr"

>chr1 AAA BBA AAA
>chr2 ABA AAA CCC TTT
>chr3 TTT CCC TCT

and finally use awk to print all the lines with "\n" as output file separator

>chr1
AAA
BBA
AAA
>chr2
ABA
AAA
CCC
>chr3
TTT
CCC
TCT