Find string then print what comes next until another string
.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ height:90px;width:728px;box-sizing:border-box;
}
0
Here's my input.file (thousands of lines):
FN545816.1 EMBL CDS 9450 9857 . + 0 ID=cds-CBE01461.1;Parent=gene-CDR20291_3551;Dbxref=EnsemblGenomes-Gn:CDR20291_3551,EnsemblGenomes-Tr:CBE01461,GOA:C9YHF8,InterPro:IPR003594,UniProtKB/TrEMBL:C9YHF8,NCBI_GP:CBE01461.1;Name=CBE01461.1;gbkey=CDS;gene=rsbW;product=anti-sigma-B factor (serine-protein kinase);protein_id=CBE01461.1;transl_table=11
I want to extract only what comes after product= up to the next ;
So, in this case, I want to get "anti-sigma-B factor (serine-protein kinase)"
I tried this:
awk '{for(i=1; i<=NF; i++) if($i~/*product=/) print $(i+1)}' input.file > output.file
but it prints only "factor" (presumably because there's no space in between "product=" and "anti-sigma-B". It doesn't print the rest neither.
I tried many previous solutions but none gave what I want.
Thank you.
awk
asked Nov 17 '18 at 1:03
ThePresidentThePresident
888
add a comment |
0
Here's my input.file (thousands of lines):
FN545816.1 EMBL CDS 9450 9857 . + 0 ID=cds-CBE01461.1;Parent=gene-CDR20291_3551;Dbxref=EnsemblGenomes-Gn:CDR20291_3551,EnsemblGenomes-Tr:CBE01461,GOA:C9YHF8,InterPro:IPR003594,UniProtKB/TrEMBL:C9YHF8,NCBI_GP:CBE01461.1;Name=CBE01461.1;gbkey=CDS;gene=rsbW;product=anti-sigma-B factor (serine-protein kinase);protein_id=CBE01461.1;transl_table=11
I want to extract only what comes after product= up to the next ;
So, in this case, I want to get "anti-sigma-B factor (serine-protein kinase)"
I tried this:
awk '{for(i=1; i<=NF; i++) if($i~/*product=/) print $(i+1)}' input.file > output.file
but it prints only "factor" (presumably because there's no space in between "product=" and "anti-sigma-B". It doesn't print the rest neither.
I tried many previous solutions but none gave what I want.
Thank you.
awk
asked Nov 17 '18 at 1:03
ThePresidentThePresident
888
give it sometime and try to select and answer out of all as a correct one to complete the thread, see this once too stackoverflow.com/help/someone-answers
– RavinderSingh13
Nov 17 '18 at 2:24
add a comment |
0
0
0
Here's my input.file (thousands of lines):
FN545816.1 EMBL CDS 9450 9857 . + 0 ID=cds-CBE01461.1;Parent=gene-CDR20291_3551;Dbxref=EnsemblGenomes-Gn:CDR20291_3551,EnsemblGenomes-Tr:CBE01461,GOA:C9YHF8,InterPro:IPR003594,UniProtKB/TrEMBL:C9YHF8,NCBI_GP:CBE01461.1;Name=CBE01461.1;gbkey=CDS;gene=rsbW;product=anti-sigma-B factor (serine-protein kinase);protein_id=CBE01461.1;transl_table=11
I want to extract only what comes after product= up to the next ;
So, in this case, I want to get "anti-sigma-B factor (serine-protein kinase)"
I tried this:
awk '{for(i=1; i<=NF; i++) if($i~/*product=/) print $(i+1)}' input.file > output.file
but it prints only "factor" (presumably because there's no space in between "product=" and "anti-sigma-B". It doesn't print the rest neither.
I tried many previous solutions but none gave what I want.
Thank you.
awk
asked Nov 17 '18 at 1:03
ThePresidentThePresident
888
Here's my input.file (thousands of lines):
FN545816.1 EMBL CDS 9450 9857 . + 0 ID=cds-CBE01461.1;Parent=gene-CDR20291_3551;Dbxref=EnsemblGenomes-Gn:CDR20291_3551,EnsemblGenomes-Tr:CBE01461,GOA:C9YHF8,InterPro:IPR003594,UniProtKB/TrEMBL:C9YHF8,NCBI_GP:CBE01461.1;Name=CBE01461.1;gbkey=CDS;gene=rsbW;product=anti-sigma-B factor (serine-protein kinase);protein_id=CBE01461.1;transl_table=11
I want to extract only what comes after product= up to the next ;
So, in this case, I want to get "anti-sigma-B factor (serine-protein kinase)"
I tried this:
awk '{for(i=1; i<=NF; i++) if($i~/*product=/) print $(i+1)}' input.file > output.file
but it prints only "factor" (presumably because there's no space in between "product=" and "anti-sigma-B". It doesn't print the rest neither.
I tried many previous solutions but none gave what I want.
Thank you.
awk
awk
asked Nov 17 '18 at 1:03
ThePresidentThePresident
888
asked Nov 17 '18 at 1:03
ThePresidentThePresident
888
asked Nov 17 '18 at 1:03
ThePresidentThePresident
888
asked Nov 17 '18 at 1:03
ThePresidentThePresident
888
asked Nov 17 '18 at 1:03
ThePresidentThePresident
888
888
give it sometime and try to select and answer out of all as a correct one to complete the thread, see this once too stackoverflow.com/help/someone-answers
– RavinderSingh13
Nov 17 '18 at 2:24
add a comment |
give it sometime and try to select and answer out of all as a correct one to complete the thread, see this once too stackoverflow.com/help/someone-answers
– RavinderSingh13
Nov 17 '18 at 2:24
give it sometime and try to select and answer out of all as a correct one to complete the thread, see this once too stackoverflow.com/help/someone-answers
– RavinderSingh13
Nov 17 '18 at 2:24
give it sometime and try to select and answer out of all as a correct one to complete the thread, see this once too stackoverflow.com/help/someone-answers
– RavinderSingh13
Nov 17 '18 at 2:24
add a comment |
1 Answer
1
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oldest
votes
1
Could you please try following.
awk 'match($0,/product=[^;]*/){print substr($0,RSTART+8,RLENGTH-8)}' Input_file
Explanation: Adding explanation for above code too now.
awk ' ##Starting awk program here.
match($0,/product=[^;]*/){ ##Using match function for awk here, where giving REGEX to match from string product= till first occurrence of ;
print substr($0,RSTART+8,RLENGTH-8) ##Printing substring whose value is from RSTART+8 to till RLENGTH-8, where RSTART and RLENGTH are out of the box keywords which will be set once REGEX condition is satisfied. RSTART mean starting point of regex and RLENGTH is length of REGEX matched.
}' Input_file ##Mentioning Input_file name here.
answered Nov 17 '18 at 2:07
RavinderSingh13RavinderSingh13
31k41639
Yes, this works perfectly, thank you! Honestly, I did not get thesubstr($0,RSTART+8,RLENGTH-8)part.
– ThePresident
Nov 17 '18 at 2:28
@ThePresident, I had added explanation to my answer too, whereRSTARTis the starting index(point) of matched regex andRLENGTHis the length of that matched REGEX. So as we knowsubstris used to get sub string then it has starting point(from where it should cut string) I have putRSTARTtillRLENGTH, is it clear now please let me know in case of any queries?
– RavinderSingh13
Nov 17 '18 at 2:30
1
Yeah makes sense now. Thank you.
– ThePresident
Nov 17 '18 at 2:32
add a comment |
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1 Answer
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Could you please try following.
awk 'match($0,/product=[^;]*/){print substr($0,RSTART+8,RLENGTH-8)}' Input_file
Explanation: Adding explanation for above code too now.
awk ' ##Starting awk program here.
match($0,/product=[^;]*/){ ##Using match function for awk here, where giving REGEX to match from string product= till first occurrence of ;
print substr($0,RSTART+8,RLENGTH-8) ##Printing substring whose value is from RSTART+8 to till RLENGTH-8, where RSTART and RLENGTH are out of the box keywords which will be set once REGEX condition is satisfied. RSTART mean starting point of regex and RLENGTH is length of REGEX matched.
}' Input_file ##Mentioning Input_file name here.
answered Nov 17 '18 at 2:07
RavinderSingh13RavinderSingh13
31k41639
Yes, this works perfectly, thank you! Honestly, I did not get thesubstr($0,RSTART+8,RLENGTH-8)part.
– ThePresident
Nov 17 '18 at 2:28
@ThePresident, I had added explanation to my answer too, whereRSTARTis the starting index(point) of matched regex andRLENGTHis the length of that matched REGEX. So as we knowsubstris used to get sub string then it has starting point(from where it should cut string) I have putRSTARTtillRLENGTH, is it clear now please let me know in case of any queries?
– RavinderSingh13
Nov 17 '18 at 2:30
1
Yeah makes sense now. Thank you.
– ThePresident
Nov 17 '18 at 2:32
add a comment |
1
Could you please try following.
awk 'match($0,/product=[^;]*/){print substr($0,RSTART+8,RLENGTH-8)}' Input_file
Explanation: Adding explanation for above code too now.
awk ' ##Starting awk program here.
match($0,/product=[^;]*/){ ##Using match function for awk here, where giving REGEX to match from string product= till first occurrence of ;
print substr($0,RSTART+8,RLENGTH-8) ##Printing substring whose value is from RSTART+8 to till RLENGTH-8, where RSTART and RLENGTH are out of the box keywords which will be set once REGEX condition is satisfied. RSTART mean starting point of regex and RLENGTH is length of REGEX matched.
}' Input_file ##Mentioning Input_file name here.
answered Nov 17 '18 at 2:07
RavinderSingh13RavinderSingh13
31k41639
Yes, this works perfectly, thank you! Honestly, I did not get thesubstr($0,RSTART+8,RLENGTH-8)part.
– ThePresident
Nov 17 '18 at 2:28
@ThePresident, I had added explanation to my answer too, whereRSTARTis the starting index(point) of matched regex andRLENGTHis the length of that matched REGEX. So as we knowsubstris used to get sub string then it has starting point(from where it should cut string) I have putRSTARTtillRLENGTH, is it clear now please let me know in case of any queries?
– RavinderSingh13
Nov 17 '18 at 2:30
1
Yeah makes sense now. Thank you.
– ThePresident
Nov 17 '18 at 2:32
add a comment |
1
1
1
Could you please try following.
awk 'match($0,/product=[^;]*/){print substr($0,RSTART+8,RLENGTH-8)}' Input_file
Explanation: Adding explanation for above code too now.
awk ' ##Starting awk program here.
match($0,/product=[^;]*/){ ##Using match function for awk here, where giving REGEX to match from string product= till first occurrence of ;
print substr($0,RSTART+8,RLENGTH-8) ##Printing substring whose value is from RSTART+8 to till RLENGTH-8, where RSTART and RLENGTH are out of the box keywords which will be set once REGEX condition is satisfied. RSTART mean starting point of regex and RLENGTH is length of REGEX matched.
}' Input_file ##Mentioning Input_file name here.
answered Nov 17 '18 at 2:07
RavinderSingh13RavinderSingh13
31k41639
Could you please try following.
awk 'match($0,/product=[^;]*/){print substr($0,RSTART+8,RLENGTH-8)}' Input_file
Explanation: Adding explanation for above code too now.
awk ' ##Starting awk program here.
match($0,/product=[^;]*/){ ##Using match function for awk here, where giving REGEX to match from string product= till first occurrence of ;
print substr($0,RSTART+8,RLENGTH-8) ##Printing substring whose value is from RSTART+8 to till RLENGTH-8, where RSTART and RLENGTH are out of the box keywords which will be set once REGEX condition is satisfied. RSTART mean starting point of regex and RLENGTH is length of REGEX matched.
}' Input_file ##Mentioning Input_file name here.
answered Nov 17 '18 at 2:07
RavinderSingh13RavinderSingh13
31k41639
edited Nov 17 '18 at 2:13
answered Nov 17 '18 at 2:07
RavinderSingh13RavinderSingh13
31k41639
answered Nov 17 '18 at 2:07
RavinderSingh13RavinderSingh13
31k41639
answered Nov 17 '18 at 2:07
RavinderSingh13RavinderSingh13
31k41639
31k41639
Yes, this works perfectly, thank you! Honestly, I did not get thesubstr($0,RSTART+8,RLENGTH-8)part.
– ThePresident
Nov 17 '18 at 2:28
@ThePresident, I had added explanation to my answer too, whereRSTARTis the starting index(point) of matched regex andRLENGTHis the length of that matched REGEX. So as we knowsubstris used to get sub string then it has starting point(from where it should cut string) I have putRSTARTtillRLENGTH, is it clear now please let me know in case of any queries?
– RavinderSingh13
Nov 17 '18 at 2:30
1
Yeah makes sense now. Thank you.
– ThePresident
Nov 17 '18 at 2:32
add a comment |
Yes, this works perfectly, thank you! Honestly, I did not get thesubstr($0,RSTART+8,RLENGTH-8)part.
– ThePresident
Nov 17 '18 at 2:28
@ThePresident, I had added explanation to my answer too, whereRSTARTis the starting index(point) of matched regex andRLENGTHis the length of that matched REGEX. So as we knowsubstris used to get sub string then it has starting point(from where it should cut string) I have putRSTARTtillRLENGTH, is it clear now please let me know in case of any queries?
– RavinderSingh13
Nov 17 '18 at 2:30
1
Yeah makes sense now. Thank you.
– ThePresident
Nov 17 '18 at 2:32
Yes, this works perfectly, thank you! Honestly, I did not get the
substr($0,RSTART+8,RLENGTH-8) part.– ThePresident
Nov 17 '18 at 2:28
Yes, this works perfectly, thank you! Honestly, I did not get the
substr($0,RSTART+8,RLENGTH-8) part.– ThePresident
Nov 17 '18 at 2:28
@ThePresident, I had added explanation to my answer too, where
RSTART is the starting index(point) of matched regex and RLENGTH is the length of that matched REGEX. So as we know substr is used to get sub string then it has starting point(from where it should cut string) I have put RSTART till RLENGTH, is it clear now please let me know in case of any queries?– RavinderSingh13
Nov 17 '18 at 2:30
@ThePresident, I had added explanation to my answer too, where
RSTART is the starting index(point) of matched regex and RLENGTH is the length of that matched REGEX. So as we know substr is used to get sub string then it has starting point(from where it should cut string) I have put RSTART till RLENGTH, is it clear now please let me know in case of any queries?– RavinderSingh13
Nov 17 '18 at 2:30
1
1
Yeah makes sense now. Thank you.
– ThePresident
Nov 17 '18 at 2:32
Yeah makes sense now. Thank you.
– ThePresident
Nov 17 '18 at 2:32
add a comment |
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give it sometime and try to select and answer out of all as a correct one to complete the thread, see this once too stackoverflow.com/help/someone-answers
– RavinderSingh13
Nov 17 '18 at 2:24