Compare two text files, extract matching rows of file2 plus additional rows
have been mocking around with this too long and tried grep, join, awk but I cant get the parameters right. Could you please help me getting the command right?
I have got two text files.
cat file1
@ABC:11:ABC:1:1111:1111:1111
@ABC:22:ABC:1:1111:4444:4444
cat file2
@ABC:11:ABC:1:1111:1111:1111 1:N:0:TCCCGCGC+AGGCGGGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:11:ABC:1:1111:2222:2222 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:3333:3333 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:4444:4444 1:N:0:TCCCGCGC+AGGCGGGG
TTTTTTTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
I would like to do the two things:
output 1) Based on file1, extract all rows that contain the strings plus two additional string.
output 2) Based on file1, extract all rows that do not contain the strings plus two additional rows - but it should only try to match lines that start with @..
Example output 1):
cat output1
@ABC:11:ABC:1:1111:1111:1111 1:N:0:TCCCGCGC+AGGCGGGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:4444:4444 1:N:0:TCCCGCGC+AGGCGGGG
TTTTTTTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Example output 2)
cat output2
@ABC:11:ABC:1:1111:2222:2222 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:3333:3333 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Many thanks for the help. Very much appreciated (no perl please ;D )!
Pat
text-processing awk sed python pattern-matching
asked 5 mins ago
PatPat
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have been mocking around with this too long and tried grep, join, awk but I cant get the parameters right. Could you please help me getting the command right?
I have got two text files.
cat file1
@ABC:11:ABC:1:1111:1111:1111
@ABC:22:ABC:1:1111:4444:4444
cat file2
@ABC:11:ABC:1:1111:1111:1111 1:N:0:TCCCGCGC+AGGCGGGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:11:ABC:1:1111:2222:2222 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:3333:3333 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:4444:4444 1:N:0:TCCCGCGC+AGGCGGGG
TTTTTTTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
I would like to do the two things:
output 1) Based on file1, extract all rows that contain the strings plus two additional string.
output 2) Based on file1, extract all rows that do not contain the strings plus two additional rows - but it should only try to match lines that start with @..
Example output 1):
cat output1
@ABC:11:ABC:1:1111:1111:1111 1:N:0:TCCCGCGC+AGGCGGGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:4444:4444 1:N:0:TCCCGCGC+AGGCGGGG
TTTTTTTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Example output 2)
cat output2
@ABC:11:ABC:1:1111:2222:2222 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:3333:3333 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Many thanks for the help. Very much appreciated (no perl please ;D )!
Pat
text-processing awk sed python pattern-matching
asked 5 mins ago
PatPat
61
New contributor
Pat is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |
have been mocking around with this too long and tried grep, join, awk but I cant get the parameters right. Could you please help me getting the command right?
I have got two text files.
cat file1
@ABC:11:ABC:1:1111:1111:1111
@ABC:22:ABC:1:1111:4444:4444
cat file2
@ABC:11:ABC:1:1111:1111:1111 1:N:0:TCCCGCGC+AGGCGGGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:11:ABC:1:1111:2222:2222 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:3333:3333 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:4444:4444 1:N:0:TCCCGCGC+AGGCGGGG
TTTTTTTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
I would like to do the two things:
output 1) Based on file1, extract all rows that contain the strings plus two additional string.
output 2) Based on file1, extract all rows that do not contain the strings plus two additional rows - but it should only try to match lines that start with @..
Example output 1):
cat output1
@ABC:11:ABC:1:1111:1111:1111 1:N:0:TCCCGCGC+AGGCGGGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:4444:4444 1:N:0:TCCCGCGC+AGGCGGGG
TTTTTTTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Example output 2)
cat output2
@ABC:11:ABC:1:1111:2222:2222 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:3333:3333 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Many thanks for the help. Very much appreciated (no perl please ;D )!
Pat
text-processing awk sed python pattern-matching
asked 5 mins ago
PatPat
61
New contributor
Pat is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
have been mocking around with this too long and tried grep, join, awk but I cant get the parameters right. Could you please help me getting the command right?
I have got two text files.
cat file1
@ABC:11:ABC:1:1111:1111:1111
@ABC:22:ABC:1:1111:4444:4444
cat file2
@ABC:11:ABC:1:1111:1111:1111 1:N:0:TCCCGCGC+AGGCGGGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:11:ABC:1:1111:2222:2222 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:3333:3333 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:4444:4444 1:N:0:TCCCGCGC+AGGCGGGG
TTTTTTTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
I would like to do the two things:
output 1) Based on file1, extract all rows that contain the strings plus two additional string.
output 2) Based on file1, extract all rows that do not contain the strings plus two additional rows - but it should only try to match lines that start with @..
Example output 1):
cat output1
@ABC:11:ABC:1:1111:1111:1111 1:N:0:TCCCGCGC+AGGCGGGG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:4444:4444 1:N:0:TCCCGCGC+AGGCGGGG
TTTTTTTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Example output 2)
cat output2
@ABC:11:ABC:1:1111:2222:2222 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@ABC:22:ABC:1:1111:3333:3333 1:N:0:TCCCGCGC+AGGCGGGG
AGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGGAGGCGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Many thanks for the help. Very much appreciated (no perl please ;D )!
Pat
text-processing awk sed python pattern-matching
text-processing awk sed python pattern-matching
asked 5 mins ago
PatPat
61
New contributor
Pat is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 5 mins ago
PatPat
61
New contributor
Pat is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 5 mins ago
PatPat
61
New contributor
Pat is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 5 mins ago
PatPat
61
asked 5 mins ago
PatPat
61
61
New contributor
Pat is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Pat is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Pat is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
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