How to use grep and sed simultaneously using pipe - awk

Question

I have 2 files
File 1
TRINITY_DN10039_c1_g1_i1 216 Brassica rapa
TRINITY_DN10270_c0_g1_i1 233 Pan paniscus
TRINITY_DN10323_c0_g1_i2 209 Corynebacterium aurimucosum ATCC 700975
.
.
TRINITY_DN10462_c0_g1_i1 257 Helwingia himalaica
TRINITY_DN10596_c0_g1_i1 205 Homo sapiens
TRINITY_DN10673_c0_g2_i2 323 Anaerococcus prevotii DSM 20548
File 2
TRINITY_DN9856_c0_g1_i1 len=467 path=[0:0-466]
GATGCGGGCCAATATGAATGTGAGATTACTAATGAATTGGGGACTAAAAA
TRINITY_DN9842_c0_g1_i1 len=208 path=[0:0-207]
AAGTAATTTTATATCACTTGTTACATCGCAATTCGTGAGTTAAACTTAAT
.
.
TRINITY_DN9897_c0_g1_i1 len=407 path=[0:0-406]
AACTTTATTAACTTGTTGTACATATTTATTAATGCAAATACATATAGAG
TRINITY_DN9803_c0_g1_i1 len=795 path=[0:0-794]
AACTAAGACAAACTTCGCGGAGCAGTTAGAAAATATTACAAGAGATTTG
I want to delete 2 lines(same line and next line) in file2 whose pattern matches with the first column words of 1st file
awk '{print $1}' file1 | sed '/here_i_want_to_insert_output_of_pipe/{N;d;}' file2

Answer 1

If the field has no special characters in the first field, like . or / or [ or ( or \ or any regex-special characters, your idea is actually not that bad:
sed "$(cut -d' ' -f1 file1 | sed 's#.*#/&/{N;d}#')" file2
cut -d' ' -f1 file1 - extract first field from file1
| sed
.* - replace anything. ie. the first field from file1
/&/{N;d} - the & is substituted for the whole thing we are replacing. So for the first field. So it becomes /<first field>/{N;d}
then wrap it around sed "<here>" file2
No so much known feature, you can use another character for /regex/ with syntax \<char>regex<char> like \!regex!. Below I use ~:
sed "$(cut -d' ' -f1 file1 | sed 's#.*#\\~&~{N;d}#')" file2
If you however do have any special characters on the first field, then if you don't care about sorting: You can replace two lines in file2 for a single line with some magic separator (I chose ! below), then sort it and sort file1, and then just join them. The -v2 makes join output unpairable lines from second file - ie. not matched lines. After that restore the newline, by replacing the magic separator ! for a newline:
join -v2 <(cut -d' ' -f1 file1 | sort) <(sed 'N;s/\n/!/' file2 | sort -k1) |
tr '!' '\n'
If the output needs to be sorted as in file2, you can number lines in file2 and re-sort the output on line numbers:
join -11 -22 -v2 <(cut -d' ' -f1 file1 | sort) <(sed 'N;s/\n/!/' file2 | nl -w1 | sort -k2) |
sort -k2 | cut -d' ' -f1,3- | tr '!' '\n'
Tested on repl

Answer 2

I would do something like this with one awk, unless file1 is really really really huge :
awk 'NR==FNR{a[$1]++; next}counter{counter--}$1 in a{counter=2}!counter' <file1> <file2>
Input :
file1
TRINITY_DN10039_c1_g1_i1 216 Brassica rapa
TRINITY_DN10270_c0_g1_i1 233 Pan paniscus
TRINITY_DN10323_c0_g1_i2 209 Corynebacterium aurimucosum ATCC 700975
hello
TRINITY_DN10462_c0_g1_i1 257 Helwingia himalaica
TRINITY_DN10596_c0_g1_i1 205 Homo sapiens
TRINITY_DN10673_c0_g2_i2 323 Anaerococcus prevotii DSM 20548
file2 :
TRINITY_DN9856_c0_g1_i1 len=467 path=[0:0-466]
GATGCGGGCCAATATGAATGTGAGATTACTAATGAATTGGGGACTAAAAA
TRINITY_DN9842_c0_g1_i1 len=208 path=[0:0-207]
AAGTAATTTTATATCACTTGTTACATCGCAATTCGTGAGTTAAACTTAAT
TRINITY_DN9897_c0_g1_i1 len=407 path=[0:0-406]
AACTTTATTAACTTGTTGTACATATTTATTAATGCAAATACATATAGAG
hello
world
TRINITY_DN9803_c0_g1_i1 len=795 path=[0:0-794]
AACTAAGACAAACTTCGCGGAGCAGTTAGAAAATATTACAAGAGATTTG
Output :
TRINITY_DN9856_c0_g1_i1 len=467 path=[0:0-466]
GATGCGGGCCAATATGAATGTGAGATTACTAATGAATTGGGGACTAAAAA
TRINITY_DN9842_c0_g1_i1 len=208 path=[0:0-207]
AAGTAATTTTATATCACTTGTTACATCGCAATTCGTGAGTTAAACTTAAT
TRINITY_DN9897_c0_g1_i1 len=407 path=[0:0-406]
AACTTTATTAACTTGTTGTACATATTTATTAATGCAAATACATATAGAG
TRINITY_DN9803_c0_g1_i1 len=795 path=[0:0-794]
AACTAAGACAAACTTCGCGGAGCAGTTAGAAAATATTACAAGAGATTTG

Answer 3

I would do this with process substitution like so:
while read -r -d '' line; do
sed -i "/^${line}/{N;d;}" file2
done < <(awk '{printf "%s\0", $1}' file1 | sed 's|[][\\/.*^$]|\\&|g')
The reason for delimiting by nullbytes rather than newlines is because it's usually the best way.
Edit:
Updated to quote special characters with \ so sed won't malfunction.