If the debugging lines are being printed then each file is being read but not processed? Thank you very much .
No. Debugging lines are being printed (along with your desired output) because you set d to a non-zero, non-null value in exon.sh. The fact that you implied that the output files only contained three lines of debugging information and none of the output you were expecting tells me that you didn't bother to try to understand how the script I gave you works. That is very discouraging. I guess I'm wasting my time here.
I have a line like this:
I want to move HTTP/1.1 200 OK to the next line and put a blank line between the two lines i.e.
How can i get it using awk?
Thanks in advance (2 Replies)
Hi All,
I was wondering if anyone knew how to dynamically change the FS in awk to accept vairiable containing a field separator. the current code is as below and does not work when i introduce the dynamic FS change :-(
validate_source_file()
{
source_file=$1
... (2 Replies)
Hi, all
I need to get fields in a line that are separated by commas, some of the fields are enclosed with double quotes, and they are supposed to be treated as a single field even if there are commas inside the quotes.
sample input:
for this line, 5 fields are supposed to be extracted, they... (8 Replies)
First, thanks for the help in previous posts... couldn't have gotten where I am now without it!
So here is what I have, I use AWK to match $1 and $2 as 1 string in file1 to $1 and $2 as 1 string in file2. Now I'm wondering if I can extend this AWK command to incorporate the following:
If $1... (4 Replies)
Hi. I'd appreciate if I can get some direction in this issue to get me going.
Datafile1:
-About 4000 records, I have to update field#4 in selected records based on a match in the key field (Field#1).
-Field #1 is the key field (servername) . # of Fields may vary
# comment
server1 bbb ccc... (2 Replies)
Hi !
input:
111|222|333|aaa|bbb|ccc
999|888|777|nnn|kkk
444|666|555|eee|ttt|ooo|ppp
With awk, I am trying to change the FS "|" to "; " only from the 4th field until the end (the number of fields vary between records).
In order to get:
111|222|333|aaa; bbb; ccc
999|888|777|nnn; kkk... (1 Reply)
Hi Experts,
i need to change delimiter from tab to ","
sample test file
cat test
A0000368 A29938511 072569352 5 Any 2 for £1.00 BUTCHERS|CAT FOOD|400G Sep 12 2012 12:00AM Jan 5 2014 11:59PM Sep 7 2012 12:00AM M 2.000 group 5
... (2 Replies)
In the below awk in the first step I default Classification NF-1 to VUS. Next, I am trying to change the value of Classification (NF) to whatever CLINSIG (NF-1) is. If there is only one condition everything works great, but if there are two conditions it does not work. Is the syntax used... (4 Replies)
In the awk below I am trying to copy the entire contents of $6 there may be multiple values seperated by a ;, to $8, if $8 is . (lines 1 and 3 are examples). If that condition $8 is not . (line2 is an example) then that line is skipped and printed as is. The awk does execute but prints the output... (3 Replies)
Discussion started by: cmccabe
3 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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Support
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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
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web:
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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)