awk to output the percentage of a field compared to length
The awk below using the sample input would output the following: Basically, it averages the text in $5 that matches if $7 < 30 . Sample Input
Output
My question is I can not seem to add the correct syntax that will also output the total # of lines in $6 that represent $5 and the % of 7 < 30 I know my words may not be all that helpful so hopefully the desired output will help. Thank you .
Desired output
the boild is only to show the math and does not need rto be included.
Last edited by cmccabe; 09-30-2015 at 05:57 PM..
Reason: fixed formatting; [mod] extra code tags, added details
Is there a command that sets a variable length?
I have a input of a variable length field but my output for that field needs to be set to 32 char.
Is there such a command?
I am on a sun box running ksh
Thanks (2 Replies)
Dear All,
1.txt (tab in between each value in a line)
a b c
a b c
a c d
you can see below, why with ~ i can output with tab, but = cannot?
# awk -F'\t' '$2 ~ /b/' 1
a b c
a b c
# awk -F'\t' '$2 = "b"' 1
a b c
a b c
a b d
... (1 Reply)
Hello Everyone,
I am stuck with one issue while working on abstract flat file which i have to use as input and load data to table.
Input Data-
------ ------------------------ ---- -----------------
WFI001 Xxxxxx Control Work Item A Number of Records
------ ------------------------... (5 Replies)
In awk, how do I print all fields with a specified output field separator?
I have tried the following, which does not print the output FS:
echo a b c d | awk 'BEGIN{OFS = ";"}{print $0}' (3 Replies)
Hi all,
I have a requirement to replace a field with a character as per the length of the field.
Suppose i have a file where second field is of 20 character length. I want to replace second field with 20 stars (*). like ********************
As the field is not a fixed one, i want to do the... (2 Replies)
Need an awk script to calculate the percentage of value field and replace
I have a input file called file.txt with the following content:
john|622.5674603562933|8|br:1;cn:3;fr:1;jp:1;us:2
andy|0.0|12|**:3;br:1;ca:2;de:2;dz:1;fr:2;nl:1
in fourth filed of input file, calulate percentage of each... (1 Reply)
I have a input file called file.txt with the following content:
john|622.5674603562933|8|br:1;cn:3;fr:1;jp:1;us:2
andy|0.0|12|**:3;br:1;ca:2;de:2;dz:1;fr:2;nl:1
in fourth filed of input file, calulate percentage of each sub filed seperated by ; semicolon and replace value with percentage .
i... (11 Replies)
I have several questions about using awk. I'm hoping someone could lend me a hand. (I'm also hoping that my questions make sense.)
I have a file that contains pipe separated data. Each line has similar data but the number of fields and the field position on each line is variable. ... (3 Replies)
The awk below produces the current output, which will add +1 to $3. However, I am trying to add the length of the matching characters between $5 and $6 to $3. I have tried using sub as a variable to store the length but am not able to do so correctly. I added comments to each line and the... (4 Replies)
Discussion started by: cmccabe
4 Replies
LEARN ABOUT DEBIAN
bio::tools::spidey::exon
Bio::Tools::Spidey::Exon(3pm) User Contributed Perl Documentation Bio::Tools::Spidey::Exon(3pm)NAME
Bio::Tools::Spidey::Exon - A single exon determined by an alignment
SYNOPSIS
# See Bio::Tools::Spidey::Results for a description of the context.
# an instance of this class is-a Bio::SeqFeature::SimilarityPair
# coordinates of the exon (recommended way):
print "exon from ", $exon->start(),
" to ", $exon->end(), "
";
# the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
print "exon from ", $exon->feature1()->start(),
" to ", $exon->feature1()->end(), "
";
# also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
print "exon from ", $exon->query()->start(),
" to ", $exon->query()->end(), "
";
# coordinates on the matching EST (recommended way):
print "matches on EST from ", $exon->est_hit()->start(),
" to ", $exon->est_hit()->end(), "
";
# the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
print "matches on EST from ", $exon->feature2()->start(),
" to ", $exon->feature2()->end(), "
";
# also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
print "exon from ", $exon->subject()->start(),
" to ", $exon->subject()->end(), "
";
DESCRIPTION
This class inherits from Bio::SeqFeature::SimilarityPair and represents an exon on a genomic sequence determined by similarity, that is, by
aligning an EST sequence (using Spidey in this case). Consequently, the notion of query and subject is always from the perspective of the
genomic sequence: query refers to the genomic seq, subject to the aligned EST hit. Because of this, $exon->start(), $exon->end() etc will
always return what you expect.
To get the coordinates on the matching EST, refer to the properties of the feature returned by est_hit().
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 - Ryan Golhar
Email golharam@umdnj.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
percentage_id
Title : percentage_id
Usage : $obj->percentage_id
Function: This is the percent id as reported by Spidey
Returns : value of percentage_id
Args :
est_hit
Title : est_hit
Usage : $est_feature = $obj->est_hit();
Function: Returns the EST hit pointing to (i.e., aligned to by Spidey) this
exon (i.e., genomic region). At present, merely a synonym for
$obj->feature2().
Returns : An Bio::SeqFeatureI implementing object.
Args :
mismatches
Title : mismatches
Usage : $obj->mismatches;
Function: Returns the mismatches of the cDNA to (i.e., aligned to by Spidey) this
exon (i.e., genomic region).
Returns : value of mismatches.
Args :
gaps
Title : gaps
Usage : $obj->gaps;
Function: Returns the gaps of the cDNA to (i.e., aligned to by Spidey) this
exon (i.e., genomic region).
Returns : value of gaps.
Args :
donor
Title : donor
Usage : $obj->donor;
Function: Returns 0 if a splice donor site does not exist, or
1 if a splice donor site exists
Returns : value of existence of donor splice site (0 or 1)
Args :
acceptor
Title : acceptor
Usage : $obj->acceptor;
Function: Returns 0 if a splice acceptor site does not exist, or
1 if a splice acceptor site exists
Returns : value of existence of acceptor splice site (0 or 1)
Args :
perl v5.14.2 2012-03-02 Bio::Tools::Spidey::Exon(3pm)