Print sets of lines that do not have a corresponding pair

Here is a somewhat involved version for awk. Some differences from the sed version from steeldriver:

1. It makes no assumptions about the ordering of the mm10 or rn5 records
2. It can deal with a missing rn5 record
3. It will output the unmatched records to stderr.
4. It is a lot more code :-)

It can be run with:

awk -f my_program.awk infile 

The code:

# find and store a header /^NM.*/ { header = $0; next } # we found an mm10 line header ~ /_rn5/ { # get the mm10 line that matches this rn5 mm_match = header sub("_rn5", "_mm10", mm_match) # if we have a previous mm10, then print the pair if (mm_match in headers) { print header print print mm_match print headers[mm_match] delete headers[mm_match] } else { headers[header] = $0 } next } # we found an mm10 line header ~ /_mm10/ { # get the rn5 line that matches this mm10 mm_match = header sub("_mm10", "_rn5", mm_match) # if we have a previous rn5, then print the pair if (mm_match in headers) { print mm_match print headers[mm_match] print header print delete headers[mm_match] } else { headers[header] = $0 } next } 

Additionally this code can be added to the end of the file to output any unmatched lines to standard error:

# The END block is here just to output anything that was unmatched END { # dump the unmatched to stderr for (header in headers) { print header > "/dev/stderr" print headers[header] > "/dev/stderr" } } 

It can be run with:

awk -f my_program.awk infile > outfile 2> unmatched 

Which will output the requested output (via standard out) into outfile, and will output the leftover input (via standard error) into unmatched. For the details of I/O redirection in all its variety, see the chapter on Redirections in the Bash reference manual.

I think what you're asking for is something that

• maintains a 4-line buffer; and
• if the thing following rn5 (up to the next newline) matches the thing following mm10 (up to the next-but-two newline) print it and start over

It's probably an ugly way to do it, but to illustrate with GNU sed:

$ sed -n -e :a \ -e '$!N; /rn5_\(.*\)\n.*\n.*mm10_\1\n/ {p;b}' \ -e '/.*\n.*\n.*\n/ D' \ -e ba infile > outfile $ diff outfile infile 8a9,10 > NM00125_rn5_0_1_4 > zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz