I think you want a lookup table from file1: $1 is the lookup key and $2 the returned value.
Now you can test existence with (key in s) or get the value with s[key] or loop through the keys with for (key in s).
I think the following captures the wanted values in file2:
Note1: the target array as 3rd argument is an extension in GNU-awk. (Maybe you want to consider perl? Then it works on all platforms that have perl.)
Note2: for a most exact string match use a "border character". I have even prepended a ";" to the input string for match() in order to ensure it exists even at the beginning.
This User Gave Thanks to MadeInGermany For This Post:
Hi Friends,
I have a file with the following values..
xyz.txt,12345.xml
abc.txt,04567.xml
cde.txt,12134.xml
I would like to extract all the 2nd column values twice as shown in the example like
12345,12345.xml
04567,04567.xml
12134,12134.xml
Please advice!!
In the formus one of... (7 Replies)
I have read another post about this issue and am wondering how to adapt it
to my own, much simpler, issue.
I have a file of user IDs like so:
333333
321321
546465
...etc
I need to take each number and use it to print records wherein the 5th
field matches the user ID pulled from the... (2 Replies)
Hi everyone,
I have file1 and file2 comma separated both.
file1 is:
Header1,Header2,Header3,Header4,Header5,Header6,Header7,Header8,Header9,Header10
Code7,,,,,,,,,
Code5,,,,,,,,,
Code3,,,,,,,,,
Code9,,,,,,,,,
Code2,,,,,,,,,file2... (17 Replies)
Hello friends,
I have a text file with many columns (no. columns vary from row to row) separated by space. I need to collect all the values from 18th column to the end from each line and group them as pairs and then numbering like below..
1. 18th-col-value 19th-col-value 2. 20th-col-value ... (5 Replies)
In the below awk I am trying to print expName only if another tag planExecuted is true. In addition to the expName I am also printing planShortID. For some reason the word experiment gets printed so I remove it with sed. I have attached the complete index.html as well as included a sample of it... (1 Reply)
The below awk is used with the attached index.html and matches the specific user id in the sub portion with path of /rundb/api/v1/plugin/49/. The command does run but the output is blank. Something changed in the file structure as it used to work.
So using the first line in the output:
... (2 Replies)
I am trying to use awk to match the NM_ in file with $1 of id which is tab-delimited. The NM_ will always be in the line of file that starts with > and be after the second _. When there is a match between each NM_ and id, then the value of $2 in id is substituted or used to update the NM_. Each NM_... (3 Replies)
I am trying to use awk to find all the $2 values in file2 which is ~30MB and tab-delimited, that are between $2 and $3 in file1 which is ~2GB and tab-delimited.
I have just found out that I need to use $1 and $2 and $3 from file1 and $1 and $2of file2 must match $1 of file1 and be in the range... (6 Replies)
In the awk below which executes as is, I am trying to add a condition that will extract the text or
value after the FR= for the lines in each line of file1 compared
to file2. As is the lines between the two files are either a match, Missing in file 1, or Missing in file2,
but I can not add the... (1 Reply)
Discussion started by: cmccabe
1 Replies
LEARN ABOUT DEBIAN
bio::seqfeature::gene::genestructurei
Bio::SeqFeature::Gene::GeneStructureI(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::GeneStructureI(3pm)NAME
Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily
complex structure of a gene
SYNOPSIS
#documentation needed
DESCRIPTION
A feature representing a gene structure.
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 - Hilmar Lapp
Email hlapp@gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
transcripts
Title : transcripts()
Usage : @transcripts = $gene->transcripts();
Function: Get the transcript features/sites of this gene structure.
See Bio::SeqFeature::Gene::TranscriptI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects
representing the promoter regions or sites.
Args :
promoters
Title : promoters()
Usage : @prom_sites = $gene->promoters();
Function: Get the promoter features/sites of this gene structure.
Note that OO-modeling of regulatory elements is not stable yet.
This means that this method might change or even disappear in a
future release. Be aware of this if you use it.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
promoter regions or sites.
Args :
exons
Title : exons()
Usage : @exons = $gene->exons();
@inital = $gene->exons('Initial');
Function: Get all exon features or all exons of specified type of this gene
structure.
Refer to the documentation of the class that produced this gene
structure object for information about the possible types.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
representing the exon regions.
Args : An optional string specifying the type of the exon.
introns
Title : introns()
Usage : @introns = $gene->introns();
Function: Get all introns of this gene structure.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
introns.
Args :
poly_A_sites
Title : poly_A_sites()
Usage : @polyAsites = $gene->poly_A_sites();
Function: Get the poly-adenylation features/sites of this gene structure.
Returns : An array of Bio::SeqFeatureI implementing objects representing the
poly-adenylation regions or sites.
Args :
utrs
Title : utrs()
Usage : @utr_sites = $gene->utrs();
Function: Get the UTR features/sites of this gene structure.
See Bio::SeqFeature::Gene::ExonI for properties of the
returned objects.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
representing the UTR regions or sites.
Args :
perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::GeneStructureI(3pm)