Hi ,
I have a typical situation. I have 4 files and with different headers (number of headers is varible ).
I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only).
For example -
File 1
H1|H2|H3|H4
11|12|13|14
21|22|23|23... (1 Reply)
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.
input.fasta:
>YAL069W-1.334 Putative promoter sequence... (6 Replies)
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)
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)
Hi. Unix rookie here. Been looking for a few days for reference documents on how BSD UNIX lays the logical file format onto a disk. Goal is to view/edit with hex editor for data repair. Lots of docs are available for how to use Unix commands (like xxd), but I want to learn the map of how Unix... (4 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)
I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
I have 5 sequences in a fasta file namely gene1.fasta as follows,
gene1.fasta
>1256
ATGTAGC
>GEP
TAGAG
>GTY578
ATGCATA
>67_iga
ATGCTGA
>90_ld
ATGCTG
I need to rename the gene1.fasta file based on the sequence position specified in list.txt as follows,
list.txt
position1=org5... (5 Replies)
Discussion started by: dineshkumarsrk
5 Replies
LEARN ABOUT DEBIAN
bio::seqio::fasta
Bio::SeqIO::fasta(3pm) User Contributed Perl Documentation Bio::SeqIO::fasta(3pm)NAME
Bio::SeqIO::fasta - fasta sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
DESCRIPTION
This object can transform Bio::Seq objects to and from fasta flat file databases.
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/
AUTHORS - Ewan Birney & Lincoln Stein
Email: birney@ebi.ac.uk
lstein@cshl.org
CONTRIBUTORS
Jason Stajich, jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object, or nothing if no more available
Args : NONE
write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: Writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of 1 or more Bio::PrimarySeqI objects
width
Title : width
Usage : $obj->width($newval)
Function: Get/Set the line width for FASTA output
Returns : value of width
Args : newvalue (optional)
preferred_id_type
Title : preferred_id_type
Usage : $obj->preferred_id_type('accession')
Function: Get/Set the preferred type of identifier to use in the ">ID" position
for FASTA output.
Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display').
Args : string when setting. This must be one of values defined in
@Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
accession, accession.version, display, primary
Throws : fatal exception if the supplied id type is not in @SEQ_ID_TYPES.
perl v5.14.2 2012-03-02 Bio::SeqIO::fasta(3pm)