10 More Discussions You Might Find Interesting
1. UNIX for Beginners Questions & Answers
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
3 Replies
2. Shell Programming and Scripting
I would like to take a fasta file formated like
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
and use command line perl to move the all sample gt 8 in length to a new file. the result would be
>0001
agttcgaggtcagaatt
>0003
ggtaacctga
cat ${sample}.fasta | perl -lane... (2 Replies)
Discussion started by: jdilts
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3. UNIX for Dummies Questions & Answers
Hi
I am looking to rename the contents of this dir, each one with a new timestamp, interval of a second for each so it the existing format is on lhs and what I want is to rename each of these to what is on rhs..hopefully it nake sense
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4. Solaris
hi,
I would like to monitor a log file, which rolls over, everytime a server is restarted.
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5. Shell Programming and Scripting
Hi All,
I have a unix shell script file as below.
My task is
a)to replace 248 to 350 and need to create a new file as BW3_350.sh
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there is no... (6 Replies)
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6. Shell Programming and Scripting
Hi all ,
I'm new to unix
I have a checked project , there exists a file called xxx.config .
now my task is to find all the files in the checked out project which references to this xxx.config file.
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Discussion started by: Gangam
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7. Shell Programming and Scripting
HI,
Please find the text below. I receive a .csv file on server. I need the comma(,) in the second column to be replaced by a semi-colon( ; ).
How to do it. Please help.
Sample text:
"1","lastname1,firstname1","xxxxxx","19/10/2009","23/10/2009","0","N","Leave"... (2 Replies)
Discussion started by: libin4u2000
2 Replies
8. Shell Programming and Scripting
find . -type f -name "*.sql" -print|xargs perl -i -pe 's/pattern/replaced/g'
this is simple logic to find and replace in multiple files & folders
Hope this helps.
Thanks
Zaheer (0 Replies)
Discussion started by: Zaheer.mic
0 Replies
9. UNIX for Dummies Questions & Answers
how to use sed command to find and replace a directory
i have a file.. which contains lot of paths ...
for eg.. file contains..
/usr/kk/rr/12345/1
/usr/kk/rr/12345/2
/usr/kk/rr/12345/3
/usr/kk/rr/12345/4
/usr/kk/rr/12345/5
/usr/kk/rr/12345/6
/usr/kk/rr/12345/7... (1 Reply)
Discussion started by: wip_vasikaran
1 Replies
10. Shell Programming and Scripting
I get a text file with 70+ columns (seperated by Tab) and about 10000 rows. The 58th Column is all numbers. But sometimes 58th columns has "/xxx=##" after the numeric data. I want to truncate this string using the script. Any Ideas...:confused: (3 Replies)
Discussion started by: gagansharma
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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)