1 PRO 3 ILE 6.816858
2 GLN 4 THR 6.763534
3 ILE 5 LEU 6.659603
4 THR 6 TRP 5.887478
5 LEU 7 GLN 5.224145
6 TRP 4 THR 5.887478
7 GLN 5 LEU 5.224145
8 ARG 10 LEU 5.922154
9 PRO 23 LEU 5.841176
10 LEU 23 LEU 4.665862
11 VAL 22 ALA 5.404240
12 THR 21 GLU 4.437617
13 ILE 66 ILE 4.792131
14 LYS 19 LEU 4.804988
15 ILE 17 GLY 5.244380
16 GLY 18 GLN 5.444090
17 GLY 15 ILE 5.244380
18 GLN 15 ILE 5.435863
19 LEU 14 LYS 4.804988
20 LYS 13 ILE 5.280103
21 GLU 12 THR 4.437617
22 ALA 83 ASN 4.773669
23 LEU 10 LEU 4.665862
24 SER 85 ILE 5.104049
25 ASP 86 GLY 5.401655
26 THR 28 ALA 5.716655
I want to print the row containg "PRO" in second column after comparing and finding the minimum value of fifth column present in all "PRO". and likewise for every other string present in second column.
I am using :
I am getting results, but I didnt understand this command....
and if there is only one string like "SER" in 2nd row, it is not printed in output file. Whereas, I want to have all strings with minimum fifth column.
Can any one plz suggest me for the same. or make me understand the command ??????
Hi everybody:
I try to print in new file selected lines from another file wich depends on the first column.
I have done a script like this:
lines=( "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "21" "31" "41" "51" "55" "57" "58" )
${lines}
for lines in ${lines}
do
awk -v ... (6 Replies)
How can I extract few lines(like 10 to 15, top 10 and last 10) from a file using perl.
I do it with sed, head and tail in unix scripting. I am new to perl. Appreciate your help. (2 Replies)
Hi,
I would like a shell script that reads all files in a directory and concatenate them. It is not a simple concatenation. The first few lines of the files should not be included. The lines to be included are the lines from where 'START HERE' appears up to the end of the file. For example, I... (4 Replies)
Hi,
I am looking to copy selected lines from a file using the vim editor. I have looked up a few resources and they have suggested to use this-
Type mk
Type: "ay'k (double quotes, <register name from a-z>, <y-yank single quote, k
You can paste those lines wherever you want with "ap
I tried... (7 Replies)
I have an if statement where I state that if there are more than one records (lines) found containing a string in a file, then it enters into a while loop to use each line for as many lines as there are and then stop.
Trouble is, I can't figure out how to move to the next instance of each line. ... (2 Replies)
I am trying to print 1st, 2nd, 13th and 14th fields of a file of line numbers from 29 to 10029. I dont know how to put this in one code. Currently I am removing the selected lines by
awk 'NR==29,NR==10029' File1 > File2
and then doing
awk '{print $1, $2, $13, $14}' File2 > File3
Can... (3 Replies)
Hi all,
I have a question for the Gurus. I apologize if this has bee shared before but I couldn't find the link.
I am trying to read parameters from an external parameter file. What I m trying to achieve is read selected lines from an external parameter file into the script. for eg my param... (4 Replies)
hi Gurus,
I have a source file with more than 10 columns ( not fixed )
I want to delete all the lines on the following condition
1) where i have first column as "UPDATE PLAN ADD RATE SCHEDULE" and fourth column as null
awk '($1=="UPDATE PLAN ADD RATE SCHEDULE" && $4=="") {print $0}'... (5 Replies)
two files: one with the line number only, and the 2nd one with line number and content, as following:
line_file.txt
1
3
5
9
23
30
content_file.txt
1|we are the world|good|great
2|easily do this by highlighting you|easily do this by highlighting you|easily do this by highlighting... (2 Replies)
Hi Guys ,
I have two files say a1 and a2 having following contents
a1
dag
wfd
a2
dag
wfd
chire
hcm
I want to delete only the lines in a2 which are in a1 and final output of a2 should be
a2
chire
hcm (6 Replies)
Discussion started by: Pradeep_1990
6 Replies
LEARN ABOUT DEBIAN
bio::phenotype::omim::omimentryallelicvariant
Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm) User Contributed Perl Documentation Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm)NAME
Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database
SYNOPSIS
use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
$av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number => ".0001",
-title => "ALCOHOL INTOLERANCE",
-symbol => "ALDH2*2",
-description => "The ALDH2*2-encoded ...",
-aa_ori => "GLU",
-aa_mut => "LYS",
-position => 487,
-additional_mutations => "IVS4DS, G-A, +1" );
DESCRIPTION
This class models the allelic variant of the OMIM database. This class is intended to be used together with a OMIM entry class.
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
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
APPENDIX
The rest of the documentation details each of the object methods.
new
Title : new
Usage : $av = Bio::Phenotype::OMIM::OMIMentryAllelicVariant->new( -number => ".0001",
-title => "ALCOHOL INTOLERANCE",
-symbol => "ALDH2*2",
-description => "The ALDH2*2-encoded ...",
-aa_ori => "GLU",
-aa_mut => "LYS",
-position => 487,
-additional_mutations => "IVS4DS, G-A, +1" );
Function: Creates a new OMIMentryAllelicVariant object.
Returns : A new OMIMentryAllelicVariant object.
Args : -number => the OMIM allelic variant number
-title => the title
-symbol => a symbol
-description => a description
-aa_ori => the original amino acid
-aa_mut => the mutated amino acid
-position => the position of the mutation
-additional_mutations => free form description of additional mutations
init
Title : init()
Usage : $av->init();
Function: Initializes this OMIMentryAllelicVariant to all "".
Returns :
Args :
number
Title : number
Usage : $av->number( ".0001" );
or
print $av->number();
Function: Set/get for the OMIM allelic variant number of this
OMIMentryAllelicVariant.
Returns : The OMIM allelic variant number.
Args : The OMIM allelic variant number (optional).
title
Title : title
Usage : $av->title( "ALCOHOL INTOLERANCE" );
or
print $av->title();
Function: Set/get for the title of this OMIMentryAllelicVariant.
Returns : The title.
Args : The title (optional).
symbol
Title : symbol
Usage : $av->symbol( "ALDH2*2" );
or
print $av->symbol();
Function: Set/get for the symbol of this OMIMentryAllelicVariant.
Returns : A symbol.
Args : A symbol (optional).
description
Title : description
Usage : $av->description( "The ALDH2*2-encoded protein has a change ..." );
or
print $av->description();
Function: Set/get for the description of this OMIMentryAllelicVariant.
Returns : A description.
Args : A description (optional).
aa_ori
Title : aa_ori
Usage : $av->aa_ori( "GLU" );
or
print $av->aa_ori();
Function: Set/get for the original amino acid(s).
Returns : The original amino acid(s).
Args : The original amino acid(s) (optional).
aa_mut
Title : aa_mut
Usage : $av->aa_mut( "LYS" );
or
print $av->aa_mut();
Function: Set/get for the mutated amino acid(s).
Returns : The mutated amino acid(s).
Args : The mutated amino acid(s) (optional).
position
Title : position
Usage : $av->position( 487 );
or
print $av->position();
Function: Set/get for the position of the mutation.
Returns : The position of the mutation.
Args : The position of the mutation (optional).
additional_mutations
Title : additional_mutations
Usage : $av->additional_mutations( "1-BP DEL, 911T" );
or
print $av->additional_mutations();
Function: Set/get for free form description of (additional) mutation(s).
Returns : description of (additional) mutation(s).
Args : description of (additional) mutation(s) (optional).
to_string
Title : to_string()
Usage : print $av->to_string();
Function: To string method for OMIMentryAllelicVariant objects.
Returns : A string representations of this OMIMentryAllelicVariant.
Args :
perl v5.14.2 2012-03-02 Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm)