@Bartus11
Hi hope you are well.
Can I ask you another question continuing from with same data set for which you have kindly provided other answers
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=
chr01 levure8 SNP 16254 16254 0.000000 . . genotype=R;reference=G;coverage=45;refAlleleCounts=33;refAlleleStarts=25;refAlleleMeanQV=20;novelAlleleCounts=10;novelAlleleStarts=6;novelAlleleMeanQV=19;diColor1=10;diColor2=32;het=1;flag=
chr01 levure5 SNP 16511 16511 0.000000 . . genotype=A;reference=G;coverage=42;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=35;novelAlleleStarts=16;novelAlleleMeanQV=19;diColor1=12;diColor2=12;het=0;flag=h4,h10,h9,
chr01 levure6 SNP 16511 16511 0.000000 . . genotype=A;reference=G;coverage=32;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=23;novelAlleleStarts=11;novelAlleleMeanQV=17;diColor1=12;diColor2=12;het=0;flag=h4,h10,h9,
Last time you helped me sort the data accoring to any ;delimited parameter of choice in the last field of each line. This time I want to know details about the genotype parameter in this feild.
So taking the above example what I want is to know is the count of each type of genotype. So my expected output for the above would be:
Code:
S=4
R=4
A=2
Genotype is always denoted by a capital A-Z letter, so I reckon the regex can be restricted to that pattern.
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)
Discussion started by: spacegoose
15 Replies
LEARN ABOUT DEBIAN
bio::variation::snp
Bio::Variation::SNP(3pm) User Contributed Perl Documentation Bio::Variation::SNP(3pm)NAME
Bio::Variation::SNP - submitted SNP
SYNOPSIS
$SNP = Bio::Variation::SNP->new ();
DESCRIPTION
Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs,
batch IDs, validation methods).
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Allen Day <allenday@ucla.edu>
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
get/set-able methods
Usage : $is = $snp->method()
Function: for getting/setting attributes
Returns : a value. probably a scalar.
Args : if you're trying to set an attribute, pass in the new value.
Methods:
--------
id
type
observed
seq_5
seq_3
ncbi_build
ncbi_chr_hits
ncbi_ctg_hits
ncbi_seq_loc
ucsc_build
ucsc_chr_hits
ucsc_ctg_hits
heterozygous
heterozygous_SE
validated
genotype
handle
batch_id
method
locus_id
symbol
mrna
protein
functional_class
is_subsnp
Title : is_subsnp
Usage : $is = $snp->is_subsnp()
Function: returns 1 if $snp is a subSNP
Returns : 1 or undef
Args : NONE
subsnp
Title : subsnp
Usage : $subsnp = $snp->subsnp()
Function: returns the currently active subSNP of $snp
Returns : Bio::Variation::SNP
Args : NONE
add_subsnp
Title : add_subsnp
Usage : $subsnp = $snp->add_subsnp()
Function: pushes the previous value returned by subsnp() onto a stack,
accessible with each_subsnp().
Sets return value of subsnp() to a new Bio::Variation::SNP
object, and returns that object.
Returns : Bio::Varitiation::SNP
Args : NONE
each_subsnp
Title : each_subsnp
Usage : @subsnps = $snp->each_subsnp()
Function: returns a list of the subSNPs of a refSNP
Returns : list
Args : NONE
perl v5.14.2 2012-03-02 Bio::Variation::SNP(3pm)
03-24-2011
