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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)
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I would like to take a fasta file formated like
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
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>0001
agttcgaggtcagaatt
>0003
ggtaacctga
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4. Solaris
hi,
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Hi All,
I have a unix shell script file as below.
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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( ; ).
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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
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10. Shell Programming and Scripting
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BP_INDEX(1p) User Contributed Perl Documentation BP_INDEX(1p)
NAME
bp_index.pl - indexes files for use by bp_fetch.pl
SYNOPSIS
bp_index.pl index_name file1 file2 etc.
DESCRIPTION
bp_index.pl builds a bioperl index for the sequence files given in the argument list, under the index name. For example
bp_index.pl nrdb /data/nrdb/nrdb.fasta
would build an index called 'nrdb' as the index name for the file nrdb.fasta, and
bp_index.pl -fmt EMBL swiss /data/swiss/*.dat
would build an index called swiss for all the files in /data/swiss which end in .dat which are in EMBL format.
The indexes are built using the Bio/Index/* modules, in particular, Bio::Index::EMBL and the Bio::Index::Fasta modules. Any script which
uses these modules can use the index. A good example script is bp_fetch which fetches sequences and pipes them to STDOUT, for example
bp_fetch swiss:ROA1_HUMAN
gets the ROA1_HUMAN sequence from the swiss index and writes it as fasta format on STDOUT.
OPTIONS
-fmt <format> - Fasta (default), swiss or EMBL
-dir <dir> - directory where the index files are found
(overrides BIOPERL_INDEX environment variable)
Options for expert use
-type <db_type> - DBM_file type.
(overrides BIOPERL_INDEX_TYPE environment variable)
-v - report every index addition (debugging)
ENVIRONMENT
bp_index and bp_fetch coordinate where the databases lie using the enviroment variable BIOPERL_INDEX. This can be overridden using the -dir
option. There is no default value, so you must use the -dir option or set BIOPERL_INDEX.
The DB type is coordinated with BIOPERL_INDEX_TYPE which if it is not there, defaults to whatever the bioperl modules have installed, which
itself defaults to SDBM_File.
USING IT YOURSELF
bp_index.pl is a script that drives the Index modules. If you want to use this script heavily in your work, if it is Perl based, it is
almost certainly better to look at the code in this script and copy it across (probably you will be more likely to want to use the bp_fetch
code).
EXTENDING IT
bp_index is just a wrapper around James Gilbert's excellent Index modules found in bioperl
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
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 - Ewan Birney
Ewan Birney <birney@ebi.ac.uk>
perl v5.14.2 2012-03-02 BP_INDEX(1p)