Hello,
A bioperl problem I thought could be done with awk: convert the fasta format (Note: the length of each row is not the same for each entry as they were combined from different files!) to tabular format.
i.e. each row has two columns: the first one is the header for the sequence name and description, the second column is the DNA sequence. This is quite common in bioinformatics daily task.
I am aware bioperl is the right tool to do the job, but I am trying to level up my awk when I read the RS variable. Not sure how to handle this situation for the RS and the FS variables.
Thanks a lot!
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Please provide script/commands to convert text file to HTML tabular format.
No need of styles and colours, just output and a heading in table is required.
Output file will be send via email and will be seen from outlook.
(script required without using awk).
output file content: (sar... (7 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
I would like to extract all entries containing the following patterns: ccccta & ccccccccc from the following infile:
>P39PT-1224_Freq_900
cccctacgacggcattggtaatggctcccgcaagccatctctcttcagccaagg
>P39PT-784_Freq_2
cccctacgacggcattggtaatggcacccgcaagccatctctcttccccccccc
>P39PT-678_Freq_5... (4 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
Discussion started by: Ibk
3 Replies
LEARN ABOUT DEBIAN
bio::tools::erpin
Bio::Tools::ERPIN(3pm) User Contributed Perl Documentation Bio::Tools::ERPIN(3pm)NAME
Bio::Tools::ERPIN - a parser for ERPIN output
SYNOPSIS
use Bio::Tools::ERPIN;
my $parser = Bio::Tools::ERPIN->new( -file => $rna_output,
-motiftag => 'protein_bind'
-desctag => 'TRAP_binding');
#parse the results
while( my $motif = $parser->next_prediction) {
# do something here
}
DESCRIPTION
Parses raw ERPIN output.
This module is not currently complete. As is, it will parse raw ERPIN long format output and pack information into
Bio::SeqFeature::Generic objects.
Several values have also been added in the 'tag' hash. These can be accessed using the following syntax:
my ($entry) = $feature->get_Annotations('SecStructure');
Added tags are :
tset - training set used for the sequence
tsetdesc - training set description line
cutoff - cutoff value used
database - name of database
dbdesc - description of database
dbratios - nucleotide ratios of database (used to calculate evalue)
descline - entire description line (in case the regex used for
sequence ID doesn't adequately catch the name
accession - accession number of sequence (if present)
logodds - logodds score value
sequence - sequence from hit, separated based on training set
See t/ERPIN.t for example usage.
At some point a more complicated feature object may be used to support this data rather than forcing most of the information into tag/value
pairs in a SeqFeature::Generic. This will hopefully allow for more flexible analysis of data (specifically RNA secondary structural data).
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 the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris Fields
Email cjfields-at-uiuc-dot-edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Tools::ERPIN->new();
Function: Builds a new Bio::Tools::ERPIN object
Returns : an instance of Bio::Tools::ERPIN
Args : -fh/-file for input filename
-motiftag => primary tag used in gene features (default 'misc_binding')
-desctag => tag used for display_name name (default 'erpin')
-srctag => source tag used in all features (default 'ERPIN')
motif_tag
Title : motiftag
Usage : $obj->motiftag($newval)
Function: Get/Set the value used for 'motif_tag', which is used for setting the
primary_tag.
Default is 'misc_binding' as set by the global $MotifTag.
'misc_binding' is used here because a conserved RNA motif is capable
of binding proteins (regulatory proteins), antisense RNA (siRNA),
small molecules (riboswitches), or nothing at all (tRNA,
terminators, etc.). It is recommended that this be changed to other
tags ('misc_RNA', 'protein_binding', 'tRNA', etc.) where appropriate.
For more information, see:
http://www.ncbi.nlm.nih.gov/collab/FT/index.html
Returns : value of motif_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
source_tag
Title : source_tag
Usage : $obj->source_tag($newval)
Function: Get/Set the value used for the 'source_tag'.
Default is 'ERPIN' as set by the global $SrcTag
Returns : value of source_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
desc_tag
Title : desc_tag
Usage : $obj->desc_tag($newval)
Function: Get/Set the value used for the query motif. This will be placed in
the tag '-display_name'. Default is 'erpin' as set by the global
$DescTag. Use this to manually set the descriptor (motif searched for).
Since there is no way for this module to tell what the motif is from the
name of the descriptor file or the ERPIN output, this should
be set every time an ERPIN object is instantiated for clarity
Returns : value of exon_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
analysis_method
Usage : $obj->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/ERPIN/i.
Returns : String
Argument : n/a
next_feature
Title : next_feature
Usage : while($gene = $obj->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the ERPIN result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Returns : A Bio::Tools::Prediction::Gene object.
Args : None (at present)
next_prediction
Title : next_prediction
Usage : while($gene = $obj->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the ERPIN result
file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::Tools::Prediction::Gene object.
Args : None (at present)
perl v5.14.2 2012-03-02 Bio::Tools::ERPIN(3pm)