@Bartus11: Thanks again for the comments and all your help .... I'll be back with more ...Hv a nice evening/day whatever fits ur local time
@ctsgnb:
Thank you too. I already knew about the uniq command but not about the -u and -d options .... guess I could have done a
Code:
man uniq
, but its much nicer to hear from you all .... I'm loving programming , even if I can only script a few lines of code ... keep the good info coming this way ... Merci (guessing ur French)
---------- Post updated at 02:59 PM ---------- Previous update was at 02:45 PM ----------
I actually have a question already ....concerning the same files we a dealing with .... now my output file contains a series of lines with 9 fields ...
In a normal file I could have done [CODEsort -n -k9CODE]
For me the complication arises because I need to sort with a parameter in the 9th field but it contains a series of information delimited by semicolons. An example is shown below ... Now say for example I wanted to sort the data by coverage, which is embedded with the other info in feild 9, how do I do that ? And would be nice if the code could tell the maximum and minimum "sorting parameter" for that particular file .... I hope I'm clear ...
Could you please help out on this
Thanks very much
Code:
chr01 levure5 SNP 12745 12745 0.000000 . . genotype=S;reference=C;coverage=91;refAlleleCounts=44;refAlleleStarts=28;refAlleleMeanQV=19;novelAlleleCounts=40;novelAlleleStarts=25;novelAlleleMeanQV=18;diColor1=22;diColor2=11;het=1;flag=
chr01 levure6 SNP 12745 12745 0.000000 . . genotype=S;reference=C;coverage=62;refAlleleCounts=29;refAlleleStarts=19;refAlleleMeanQV=19;novelAlleleCounts=32;novelAlleleStarts=20;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01 levure7 SNP 12745 12745 0.000000 . . genotype=S;reference=C;coverage=24;refAlleleCounts=9;refAlleleStarts=8;refAlleleMeanQV=23;novelAlleleCounts=13;novelAlleleStarts=12;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01 levure8 SNP 12745 12745 0.000000 . . genotype=S;reference=C;coverage=37;refAlleleCounts=18;refAlleleStarts=17;refAlleleMeanQV=18;novelAlleleCounts=18;novelAlleleStarts=13;novelAlleleMeanQV=20;diColor1=11;diColor2=22;het=1;flag=
chr01 levure5 SNP 16254 16254 0.000000 . . genotype=R;reference=G;coverage=111;refAlleleCounts=82;refAlleleStarts=41;refAlleleMeanQV=18;novelAlleleCounts=28;novelAlleleStarts=9;novelAlleleMeanQV=18;diColor1=10;diColor2=32;het=1;flag=
chr01 levure6 SNP 16254 16254 0.000000 . . genotype=R;reference=G;coverage=96;refAlleleCounts=72;refAlleleStarts=38;refAlleleMeanQV=17;novelAlleleCounts=24;novelAlleleStarts=6;novelAlleleMeanQV=15;diColor1=10;diColor2=32;het=1;flag=
chr01 levure7 SNP 16254 16254 0.000000 . . genotype=R;reference=G;coverage=32;refAlleleCounts=20;refAlleleStarts=18;refAlleleMeanQV=19;novelAlleleCounts=12;novelAlleleStarts=5;novelAlleleMeanQV=17;diColor1=10;diColor2=32;het=1;flag=
---------- Post updated at 03:01 PM ---------- Previous update was at 02:59 PM ----------
I would like to have control over any sorting parameter of choice within field 9 and not just coverage ...just to clarify
Cheers
---------- Post updated at 04:21 PM ---------- Previous update was at 03:01 PM ----------
@Bartus11
Hi mate ... I dont understand one thing in your code .... how is it possible to store the results of different commands in the same variable x in ur command ?? ... I mean its possible coz the code works but can u explain ?
Code:
x=`sort file_1`;for i in file_2 file_3; do x=`comm -12 <(echo "$x") <(sort $i)`; done; echo "$x"
Hello,
I have a bash shell script and I use awk to print certain columns of one file and direct the output to another file. If I do a less or cat on the file it looks correct, but if I email the file and open it with Outlook the lines outputted by awk are concatenated.
Here is my awk line:... (6 Replies)
Hi All,
I have a very huge file (4GB) which has duplicate lines. I want to delete duplicate lines leaving unique lines. Sort, uniq, awk '!x++' are not working as its running out of buffer space.
I dont know if this works : I want to read each line of the File in a For Loop, and want to... (16 Replies)
Hi friends,
I have multiple files. For now, let's say I have two of the following style
cat 1.txt
cat 2.txt
output.txt
Please note that my files are not sorted and in the output file I need another extra column that says the file from which it is coming. I have more than 100... (19 Replies)
hi
i have used comm -13 <(sort 1.txt) <(sort 2.txt) option to get the unique lines that are present in file 2 but not in file 1. but some how i am getting the entire file 2. i would expect few but not all uncommon lines fro my dat. is there anything wrong with the way i used the command?
my... (1 Reply)
hi
my problem is little complicated one. i have 2 files which appear like this
file 1
abbsss:aa:22:34:as akl abc 1234
mkilll:as:ss:23:qs asc abc 0987
mlopii:cd:wq:24:as asd abc 7866
file2
lkoaa:as:24:32:sa alk abc 3245
lkmo:as:34:43:qs qsa abc 0987
kloia:ds:45:56:sa acq abc 7805
i... (5 Replies)
Hello everyone,
Maybe somebody could help me with an awk script.
I have this input (field separator is comma ","):
547894982,M|N|J,U|Q|P,98,101,0,1,1
234900027,M|N|J,U|Q|P,98,101,0,1,1
234900023,M|N|J,U|Q|P,98,54,3,1,1
234900028,M|H|J,S|Q|P,98,101,0,1,1
234900030,M|N|J,U|F|P,98,101,0,1,1... (2 Replies)
file 1
Sun Mar 17 00:01:33 2013 submit , Name="1234"
Sun Mar 17 00:01:33 2013 submit , Name="1344"
Sun Mar 17 00:01:33 2013 submit , Name="1124"
..
..
..
..
Sun Mar 17 00:01:33 2013 submit , Name="8901"
file 2
Sun Mar 17 00:02:47 2013 1234 execute SUCCEEDED
Sun Mar 17... (24 Replies)
I would like to print unique lines without sort or unique. Unfortunately the server I am working on does not have sort or unique. I have not been able to contact the administrator of the server to ask him to add it for several weeks. (7 Replies)
I have a directory of files, I can show the number of lines in each file and order them from lowest to highest with:
wc -l *|sort
15263 Image.txt
16401 reference.txt
40459 richtexteditor.txt
How can I also print the number of unique lines in each file?
15263 1401 Image.txt
16401... (15 Replies)
03-21-2011
...Hv a nice evening/day whatever fits ur local time