Selectively retrieve portions of a large file if a condition is met
Clash Royale CLAN TAG#URR8PPP
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I have a large file with many sections like this:
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol.
Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 33134_Pseudomonas_10M)
Pr(w>1) post mean +- SE for w
271 A 0.911 1.524 +- 0.000
369 D 0.955* 1.467 +- 0.153
492 S 0.916 1.439 +- 0.203
The grid (...)
I need a command that says something like: if after "BEB" and before "The grid" there is a "*" or "**" right after a number, print that whole row and add what is after "(amino acids refer to 1st sequence:" and before ")" in a new column. For example:
369 D 0.955* 1.467 +- 0.153 33134_Pseudomonas_10M
note: if there were two rows with "*" and/or "**" on the same section, I only need the added text once, Example:
369 D 0.955* 1.467 +- 0.153 33134_Pseudomonas_10M
378 R 0.987* 2.323 +- 0.254
text-processing text-formatting bioinformatics
asked Nov 21 at 23:07
Manuel
1399
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up vote
0
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I have a large file with many sections like this:
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol.
Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 33134_Pseudomonas_10M)
Pr(w>1) post mean +- SE for w
271 A 0.911 1.524 +- 0.000
369 D 0.955* 1.467 +- 0.153
492 S 0.916 1.439 +- 0.203
The grid (...)
I need a command that says something like: if after "BEB" and before "The grid" there is a "*" or "**" right after a number, print that whole row and add what is after "(amino acids refer to 1st sequence:" and before ")" in a new column. For example:
369 D 0.955* 1.467 +- 0.153 33134_Pseudomonas_10M
note: if there were two rows with "*" and/or "**" on the same section, I only need the added text once, Example:
369 D 0.955* 1.467 +- 0.153 33134_Pseudomonas_10M
378 R 0.987* 2.323 +- 0.254
text-processing text-formatting bioinformatics
asked Nov 21 at 23:07
Manuel
1399
1
this could do itawk '/BEB/,/The grid/)/,"")==2) seq=$0; else if($3~/^[0-9.]+*+$/) print $0, seq; seq = "" ' the_file. but it's hard to know from your snippet. You should probably make the regexps (/BEB/, etc) more narrow.
– mosvy
Nov 21 at 23:29
Worked perfectly. Thanks @mosvy!
– Manuel
Nov 21 at 23:36
add a comment |
up vote
0
down vote
favorite
up vote
0
down vote
favorite
I have a large file with many sections like this:
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol.
Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 33134_Pseudomonas_10M)
Pr(w>1) post mean +- SE for w
271 A 0.911 1.524 +- 0.000
369 D 0.955* 1.467 +- 0.153
492 S 0.916 1.439 +- 0.203
The grid (...)
I need a command that says something like: if after "BEB" and before "The grid" there is a "*" or "**" right after a number, print that whole row and add what is after "(amino acids refer to 1st sequence:" and before ")" in a new column. For example:
369 D 0.955* 1.467 +- 0.153 33134_Pseudomonas_10M
note: if there were two rows with "*" and/or "**" on the same section, I only need the added text once, Example:
369 D 0.955* 1.467 +- 0.153 33134_Pseudomonas_10M
378 R 0.987* 2.323 +- 0.254
text-processing text-formatting bioinformatics
asked Nov 21 at 23:07
Manuel
1399
I have a large file with many sections like this:
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol.
Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 33134_Pseudomonas_10M)
Pr(w>1) post mean +- SE for w
271 A 0.911 1.524 +- 0.000
369 D 0.955* 1.467 +- 0.153
492 S 0.916 1.439 +- 0.203
The grid (...)
I need a command that says something like: if after "BEB" and before "The grid" there is a "*" or "**" right after a number, print that whole row and add what is after "(amino acids refer to 1st sequence:" and before ")" in a new column. For example:
369 D 0.955* 1.467 +- 0.153 33134_Pseudomonas_10M
note: if there were two rows with "*" and/or "**" on the same section, I only need the added text once, Example:
369 D 0.955* 1.467 +- 0.153 33134_Pseudomonas_10M
378 R 0.987* 2.323 +- 0.254
text-processing text-formatting bioinformatics
text-processing text-formatting bioinformatics
asked Nov 21 at 23:07
Manuel
1399
asked Nov 21 at 23:07
Manuel
1399
edited Nov 21 at 23:13
asked Nov 21 at 23:07
Manuel
1399
asked Nov 21 at 23:07
Manuel
1399
asked Nov 21 at 23:07
Manuel
1399
1399
1
this could do itawk '/BEB/,/The grid/)/,"")==2) seq=$0; else if($3~/^[0-9.]+*+$/) print $0, seq; seq = "" ' the_file. but it's hard to know from your snippet. You should probably make the regexps (/BEB/, etc) more narrow.
– mosvy
Nov 21 at 23:29
Worked perfectly. Thanks @mosvy!
– Manuel
Nov 21 at 23:36
add a comment |
1
this could do itawk '/BEB/,/The grid/)/,"")==2) seq=$0; else if($3~/^[0-9.]+*+$/) print $0, seq; seq = "" ' the_file. but it's hard to know from your snippet. You should probably make the regexps (/BEB/, etc) more narrow.
– mosvy
Nov 21 at 23:29
Worked perfectly. Thanks @mosvy!
– Manuel
Nov 21 at 23:36
1
1
this could do it
awk '/BEB/,/The grid/)/,"")==2) seq=$0; else if($3~/^[0-9.]+*+$/) print $0, seq; seq = "" ' the_file. but it's hard to know from your snippet. You should probably make the regexps (/BEB/, etc) more narrow.– mosvy
Nov 21 at 23:29
this could do it
awk '/BEB/,/The grid/)/,"")==2) seq=$0; else if($3~/^[0-9.]+*+$/) print $0, seq; seq = "" ' the_file. but it's hard to know from your snippet. You should probably make the regexps (/BEB/, etc) more narrow.– mosvy
Nov 21 at 23:29
Worked perfectly. Thanks @mosvy!
– Manuel
Nov 21 at 23:36
Worked perfectly. Thanks @mosvy!
– Manuel
Nov 21 at 23:36
add a comment |
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this could do it
awk '/BEB/,/The grid/)/,"")==2) seq=$0; else if($3~/^[0-9.]+*+$/) print $0, seq; seq = "" ' the_file. but it's hard to know from your snippet. You should probably make the regexps (/BEB/, etc) more narrow.– mosvy
Nov 21 at 23:29
Worked perfectly. Thanks @mosvy!
– Manuel
Nov 21 at 23:36