Sort unix alphabetically then numerically, not working as I intended
Clash Royale CLAN TAG#URR8PPP
Sorry if this is a duplicate question, but I could not find the answer that I am looking for here or in the documentation.
I have a file that looks like the following:
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr4_oligo95 50 100
chr5_oligo1 50 100
chr4_oligo4 150 200
The desired output looks like:
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo95 50 100
chr4_oligo4 150 200
chr5_oligo1 50 100
The pattern at the start (e.g. chr#_oligo#) only matters in terms of the chr#, meaning that all chr1 should be first, then chr2, then chr3, etc., but I would like to sort those substrings numerically in groups as shown by the desired output above. So, I would like to know how to sort alphabetically in the case of the first column, and then keeping that order (chr1->chrN), sort each chunk of data numerically.
I apologize if my wording is not the best for this issue or if it is a duplicate. Trying
sort -k1,1 -nk2
does properly sort numerically, but does not keep the first sort intact (jumbles up the first column and places together all lines with columns 2 and 3 being like:
50 100
I am using Mac OS X.
EDIT: I want changed some of the examples in the first column to show more of what I'm looking for. gsort -V worked great if the name in the first column is in numerical order, but in my data set, it isn't always the case.
I would like to essentially sort each subgroup (in this case, chr1, chr2, etc) by column 2 iteratively. I realize this can be easily done by doing a grep for each and then sorting it on column 2, but I would like to know if sort or another unix command could accomplish this alone.
text-processing sort
add a comment |
Sorry if this is a duplicate question, but I could not find the answer that I am looking for here or in the documentation.
I have a file that looks like the following:
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr4_oligo95 50 100
chr5_oligo1 50 100
chr4_oligo4 150 200
The desired output looks like:
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo95 50 100
chr4_oligo4 150 200
chr5_oligo1 50 100
The pattern at the start (e.g. chr#_oligo#) only matters in terms of the chr#, meaning that all chr1 should be first, then chr2, then chr3, etc., but I would like to sort those substrings numerically in groups as shown by the desired output above. So, I would like to know how to sort alphabetically in the case of the first column, and then keeping that order (chr1->chrN), sort each chunk of data numerically.
I apologize if my wording is not the best for this issue or if it is a duplicate. Trying
sort -k1,1 -nk2
does properly sort numerically, but does not keep the first sort intact (jumbles up the first column and places together all lines with columns 2 and 3 being like:
50 100
I am using Mac OS X.
EDIT: I want changed some of the examples in the first column to show more of what I'm looking for. gsort -V worked great if the name in the first column is in numerical order, but in my data set, it isn't always the case.
I would like to essentially sort each subgroup (in this case, chr1, chr2, etc) by column 2 iteratively. I realize this can be easily done by doing a grep for each and then sorting it on column 2, but I would like to know if sort or another unix command could accomplish this alone.
text-processing sort
1
sort -V -k1,1 -k2 file
withgsort
(part ofcoreutils
)
– don_crissti
Sep 29 '16 at 20:47
See unix.stackexchange.com/a/289487/117549
– Jeff Schaller
Sep 29 '16 at 21:17
@JeffSchaller not what I was looking for. Moving the n around does not give the input I would like. Thank you though.
– implication
Sep 30 '16 at 1:03
@don_crissti I ran "brew install coreutils" on my terminal, and had to install Xcode. This works great! Is there a way to call gsort without typing it? I read that the sort command should be changed to call gsort instead but that does not work for me (invalid option error, meaning it is still calling the OS X sort and not coreutils version.) Thank you! I am changing the question a bit because it seems -V only works if the first column is in a numerical order. This is not always the case. I will change around my question.
– implication
Sep 30 '16 at 1:17
add a comment |
Sorry if this is a duplicate question, but I could not find the answer that I am looking for here or in the documentation.
I have a file that looks like the following:
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr4_oligo95 50 100
chr5_oligo1 50 100
chr4_oligo4 150 200
The desired output looks like:
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo95 50 100
chr4_oligo4 150 200
chr5_oligo1 50 100
The pattern at the start (e.g. chr#_oligo#) only matters in terms of the chr#, meaning that all chr1 should be first, then chr2, then chr3, etc., but I would like to sort those substrings numerically in groups as shown by the desired output above. So, I would like to know how to sort alphabetically in the case of the first column, and then keeping that order (chr1->chrN), sort each chunk of data numerically.
I apologize if my wording is not the best for this issue or if it is a duplicate. Trying
sort -k1,1 -nk2
does properly sort numerically, but does not keep the first sort intact (jumbles up the first column and places together all lines with columns 2 and 3 being like:
50 100
I am using Mac OS X.
EDIT: I want changed some of the examples in the first column to show more of what I'm looking for. gsort -V worked great if the name in the first column is in numerical order, but in my data set, it isn't always the case.
I would like to essentially sort each subgroup (in this case, chr1, chr2, etc) by column 2 iteratively. I realize this can be easily done by doing a grep for each and then sorting it on column 2, but I would like to know if sort or another unix command could accomplish this alone.
text-processing sort
Sorry if this is a duplicate question, but I could not find the answer that I am looking for here or in the documentation.
I have a file that looks like the following:
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr4_oligo95 50 100
chr5_oligo1 50 100
chr4_oligo4 150 200
The desired output looks like:
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo95 50 100
chr4_oligo4 150 200
chr5_oligo1 50 100
The pattern at the start (e.g. chr#_oligo#) only matters in terms of the chr#, meaning that all chr1 should be first, then chr2, then chr3, etc., but I would like to sort those substrings numerically in groups as shown by the desired output above. So, I would like to know how to sort alphabetically in the case of the first column, and then keeping that order (chr1->chrN), sort each chunk of data numerically.
I apologize if my wording is not the best for this issue or if it is a duplicate. Trying
sort -k1,1 -nk2
does properly sort numerically, but does not keep the first sort intact (jumbles up the first column and places together all lines with columns 2 and 3 being like:
50 100
I am using Mac OS X.
EDIT: I want changed some of the examples in the first column to show more of what I'm looking for. gsort -V worked great if the name in the first column is in numerical order, but in my data set, it isn't always the case.
I would like to essentially sort each subgroup (in this case, chr1, chr2, etc) by column 2 iteratively. I realize this can be easily done by doing a grep for each and then sorting it on column 2, but I would like to know if sort or another unix command could accomplish this alone.
text-processing sort
text-processing sort
edited Aug 1 '17 at 6:25
BitsOfNix
4,14821832
4,14821832
asked Sep 29 '16 at 20:37
implicationimplication
113
113
1
sort -V -k1,1 -k2 file
withgsort
(part ofcoreutils
)
– don_crissti
Sep 29 '16 at 20:47
See unix.stackexchange.com/a/289487/117549
– Jeff Schaller
Sep 29 '16 at 21:17
@JeffSchaller not what I was looking for. Moving the n around does not give the input I would like. Thank you though.
– implication
Sep 30 '16 at 1:03
@don_crissti I ran "brew install coreutils" on my terminal, and had to install Xcode. This works great! Is there a way to call gsort without typing it? I read that the sort command should be changed to call gsort instead but that does not work for me (invalid option error, meaning it is still calling the OS X sort and not coreutils version.) Thank you! I am changing the question a bit because it seems -V only works if the first column is in a numerical order. This is not always the case. I will change around my question.
– implication
Sep 30 '16 at 1:17
add a comment |
1
sort -V -k1,1 -k2 file
withgsort
(part ofcoreutils
)
– don_crissti
Sep 29 '16 at 20:47
See unix.stackexchange.com/a/289487/117549
– Jeff Schaller
Sep 29 '16 at 21:17
@JeffSchaller not what I was looking for. Moving the n around does not give the input I would like. Thank you though.
– implication
Sep 30 '16 at 1:03
@don_crissti I ran "brew install coreutils" on my terminal, and had to install Xcode. This works great! Is there a way to call gsort without typing it? I read that the sort command should be changed to call gsort instead but that does not work for me (invalid option error, meaning it is still calling the OS X sort and not coreutils version.) Thank you! I am changing the question a bit because it seems -V only works if the first column is in a numerical order. This is not always the case. I will change around my question.
– implication
Sep 30 '16 at 1:17
1
1
sort -V -k1,1 -k2 file
with gsort
(part of coreutils
)– don_crissti
Sep 29 '16 at 20:47
sort -V -k1,1 -k2 file
with gsort
(part of coreutils
)– don_crissti
Sep 29 '16 at 20:47
See unix.stackexchange.com/a/289487/117549
– Jeff Schaller
Sep 29 '16 at 21:17
See unix.stackexchange.com/a/289487/117549
– Jeff Schaller
Sep 29 '16 at 21:17
@JeffSchaller not what I was looking for. Moving the n around does not give the input I would like. Thank you though.
– implication
Sep 30 '16 at 1:03
@JeffSchaller not what I was looking for. Moving the n around does not give the input I would like. Thank you though.
– implication
Sep 30 '16 at 1:03
@don_crissti I ran "brew install coreutils" on my terminal, and had to install Xcode. This works great! Is there a way to call gsort without typing it? I read that the sort command should be changed to call gsort instead but that does not work for me (invalid option error, meaning it is still calling the OS X sort and not coreutils version.) Thank you! I am changing the question a bit because it seems -V only works if the first column is in a numerical order. This is not always the case. I will change around my question.
– implication
Sep 30 '16 at 1:17
@don_crissti I ran "brew install coreutils" on my terminal, and had to install Xcode. This works great! Is there a way to call gsort without typing it? I read that the sort command should be changed to call gsort instead but that does not work for me (invalid option error, meaning it is still calling the OS X sort and not coreutils version.) Thank you! I am changing the question a bit because it seems -V only works if the first column is in a numerical order. This is not always the case. I will change around my question.
– implication
Sep 30 '16 at 1:17
add a comment |
2 Answers
2
active
oldest
votes
sort -k1,1 -nk2
is the same as sort -k1,1 -n -k2
, same as sort -n -k1,1 -k2
, as in the numerical sorting is turned on globally, for all the keys.
To sort the 2nd key only numerically, you need to add n
to that sort key description as in:
sort -k1,1 -k2n
Or:
sort -k1,1 -k2,2n
With n
and with the default field separator 2
is the same as 2,2
though. 2
would be the part of the line starting from the second field, but when interpreted as a number, that's the same as the second field alone (2,2
).
Here, you could also sort numerically on the number that is after chr
and then alphabetically on the rest of the first field and then numerically on the second field with:
sort -k1.4n -k1,1 -k2n
add a comment |
sorting alphabetically on the 1st field, and numerically on the 2nd gives (in your output, -- chr4_oligo95 is before ch4_oligo4)
sort -k1,1 -k2n,2n file
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo4 150 200
chr4_oligo95 50 100
chr5_oligo1 50 100
add a comment |
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2 Answers
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2 Answers
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oldest
votes
sort -k1,1 -nk2
is the same as sort -k1,1 -n -k2
, same as sort -n -k1,1 -k2
, as in the numerical sorting is turned on globally, for all the keys.
To sort the 2nd key only numerically, you need to add n
to that sort key description as in:
sort -k1,1 -k2n
Or:
sort -k1,1 -k2,2n
With n
and with the default field separator 2
is the same as 2,2
though. 2
would be the part of the line starting from the second field, but when interpreted as a number, that's the same as the second field alone (2,2
).
Here, you could also sort numerically on the number that is after chr
and then alphabetically on the rest of the first field and then numerically on the second field with:
sort -k1.4n -k1,1 -k2n
add a comment |
sort -k1,1 -nk2
is the same as sort -k1,1 -n -k2
, same as sort -n -k1,1 -k2
, as in the numerical sorting is turned on globally, for all the keys.
To sort the 2nd key only numerically, you need to add n
to that sort key description as in:
sort -k1,1 -k2n
Or:
sort -k1,1 -k2,2n
With n
and with the default field separator 2
is the same as 2,2
though. 2
would be the part of the line starting from the second field, but when interpreted as a number, that's the same as the second field alone (2,2
).
Here, you could also sort numerically on the number that is after chr
and then alphabetically on the rest of the first field and then numerically on the second field with:
sort -k1.4n -k1,1 -k2n
add a comment |
sort -k1,1 -nk2
is the same as sort -k1,1 -n -k2
, same as sort -n -k1,1 -k2
, as in the numerical sorting is turned on globally, for all the keys.
To sort the 2nd key only numerically, you need to add n
to that sort key description as in:
sort -k1,1 -k2n
Or:
sort -k1,1 -k2,2n
With n
and with the default field separator 2
is the same as 2,2
though. 2
would be the part of the line starting from the second field, but when interpreted as a number, that's the same as the second field alone (2,2
).
Here, you could also sort numerically on the number that is after chr
and then alphabetically on the rest of the first field and then numerically on the second field with:
sort -k1.4n -k1,1 -k2n
sort -k1,1 -nk2
is the same as sort -k1,1 -n -k2
, same as sort -n -k1,1 -k2
, as in the numerical sorting is turned on globally, for all the keys.
To sort the 2nd key only numerically, you need to add n
to that sort key description as in:
sort -k1,1 -k2n
Or:
sort -k1,1 -k2,2n
With n
and with the default field separator 2
is the same as 2,2
though. 2
would be the part of the line starting from the second field, but when interpreted as a number, that's the same as the second field alone (2,2
).
Here, you could also sort numerically on the number that is after chr
and then alphabetically on the rest of the first field and then numerically on the second field with:
sort -k1.4n -k1,1 -k2n
edited Sep 30 '16 at 7:50
answered Sep 30 '16 at 7:24
Stéphane ChazelasStéphane Chazelas
302k56568922
302k56568922
add a comment |
add a comment |
sorting alphabetically on the 1st field, and numerically on the 2nd gives (in your output, -- chr4_oligo95 is before ch4_oligo4)
sort -k1,1 -k2n,2n file
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo4 150 200
chr4_oligo95 50 100
chr5_oligo1 50 100
add a comment |
sorting alphabetically on the 1st field, and numerically on the 2nd gives (in your output, -- chr4_oligo95 is before ch4_oligo4)
sort -k1,1 -k2n,2n file
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo4 150 200
chr4_oligo95 50 100
chr5_oligo1 50 100
add a comment |
sorting alphabetically on the 1st field, and numerically on the 2nd gives (in your output, -- chr4_oligo95 is before ch4_oligo4)
sort -k1,1 -k2n,2n file
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo4 150 200
chr4_oligo95 50 100
chr5_oligo1 50 100
sorting alphabetically on the 1st field, and numerically on the 2nd gives (in your output, -- chr4_oligo95 is before ch4_oligo4)
sort -k1,1 -k2n,2n file
chr1_oligo1 50 100
chr1_oligo256 150 200
chr1_oligo6 3500 3550
chr2_oligo1234 700 750
chr2_oligo1236 750 800
chr4_oligo4 150 200
chr4_oligo95 50 100
chr5_oligo1 50 100
answered Sep 30 '16 at 13:21
jai_sjai_s
1,31036
1,31036
add a comment |
add a comment |
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1
sort -V -k1,1 -k2 file
withgsort
(part ofcoreutils
)– don_crissti
Sep 29 '16 at 20:47
See unix.stackexchange.com/a/289487/117549
– Jeff Schaller
Sep 29 '16 at 21:17
@JeffSchaller not what I was looking for. Moving the n around does not give the input I would like. Thank you though.
– implication
Sep 30 '16 at 1:03
@don_crissti I ran "brew install coreutils" on my terminal, and had to install Xcode. This works great! Is there a way to call gsort without typing it? I read that the sort command should be changed to call gsort instead but that does not work for me (invalid option error, meaning it is still calling the OS X sort and not coreutils version.) Thank you! I am changing the question a bit because it seems -V only works if the first column is in a numerical order. This is not always the case. I will change around my question.
– implication
Sep 30 '16 at 1:17