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 .
Code:
awk '{if(len==0){last=$5;total=$7;len=1;getline}if($5!=last){printf("%s\t%f\n", last, total/len);last=$5;total=$7;len=1}else{total+=$7;len+=1}}END{printf("%s\t%f\n", last, total/len)}' Input.txt > output.txt
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
Code:
ID Average Reads % of Baits
AGRN:exon.1 4.5714285 3.16742 (221 (# of lines in $6 / the # 0f lines < 30 in $7)
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)
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Input Data-
------ ------------------------ ---- -----------------
WFI001 Xxxxxx Control Work Item A Number of Records
------ ------------------------... (5 Replies)
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I have tried the following, which does not print the output FS:
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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
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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)
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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::seqfeature::gene::intron
Bio::SeqFeature::Gene::Intron(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::Intron(3pm)NAME
Bio::SeqFeature::Gene::Intron - An intron feature
SYNOPSIS
Give standard usage here
DESCRIPTION
Describe the object here
FEEDBACK
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AUTHOR - David Block
Email dblock@gene.pbi.nrc.ca
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
upstream_Exon
Title : upstream_Exon
Usage : $intron->upstream_Exon()
Function: exon upstream of the intron
Returns : Bio::EnsEMBL::Exon
Args :
downstream_Exon
Title : downstream_Exon
Usage : $intron->downstream_Exon()
Function: exon downstream of the intron
Returns : Bio::EnsEMBL::Exon
Args :
phase
Title : phase
Usage : $intron->phase()
Function: returns the phase of the intron(where it interrupts the codon)
Returns : int(0,1,2)
Args :
acceptor_splice_site
Title : acceptor_splice_site
Usage : $intron->acceptor_splice_site(21,3)
Function: returns the sequence corresponding to the
consensus acceptor splice site. If start and
end are provided, it will number of base pairs
left and right of the canonical AG. Here 21 means
21 bp into intron and 3 means 3 bp into the exon.
--Intron--21----|AG|-3-----Exon
Defaults to 21,3
Returns : Bio::Seq
Args : start and end
donor_splice_site
Title : donor_splice_site
Usage : $intron->donor_splice_site(3,6)
Function: returns the sequence corresponding to the
consensus donor splice site. If start and
end are provided, it will number of base pairs
left and right of the canonical GT. Here 3 means
3 bp into exon and 6 means 6 bp into the intron.
--Exon-3--|GT|-6----Intron-
Defaults to 3,6
Returns : Bio::Seq
Args : start and end
perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::Intron(3pm)