Hi everyone,
I need to know how to remove a chunk of codes from a file
for instance i have couple of lines which are commented out of the file and i need to remove that block. here is the example
--#------------------------------------------------------------------
--# File name= ... (5 Replies)
Hi,
I do have a TAB delimted text file with the following format.
1 (- identifier of each group. this text is not present in the file only number)
1 3 4 65 56 WERTF
2 3 4 56 56 GHTYHU
3 3 5 64 23 VMFKLG
2
1 3 4 65 56 DGTEYDH
2 3 4 56 56 FJJJCKC
3 3 5 64 23 FNNNCHD
3
1 3 4 65 56 JDHJDH... (9 Replies)
Hi all,
I have the following script, but are not too sure about the syntax to complete the script.
In essence, the script must connect to a SFTP server at a client site with username and password located in a file on my server.
Then change to the appropriate directory.
Pull the data to the... (1 Reply)
Hi All
I wanted to know how to effectively delete some columns in a large tab delimited file.
I have a file that contains 5 columns and almost 100,000 rows
3456 f g t t
3456 g h
456 f h
4567 f g h z
345 f g
567 h j k lThis is a very large data file and tab delimited.
I need... (2 Replies)
Hi All,
I need some help to effectively parse out a subset of results from a big results file.
Below is an example of the text file. Each block that I need to parse starts with "Output of GENE for sequence file 100.fasta" (next block starts with another number). I have given the portion of... (8 Replies)
Hi Gurus,
I need some help in extracting some of these information and massage it into the desired output as shown below.
I need to extract the last row with the header in below sample which is usually the most recent date, for example:
2012-06-01 142356 mb 519 -219406 mb 1 ... (9 Replies)
Hi ,
I am getting file name like
ABC_DATA_CUSTIOMERS_20120617.dat
ABC_DATA_PRODUCTS_20120617.dat
Need to convert
CUSTIOMERS.dat
PRODUCTS.dat
Help me how to do this. (7 Replies)
Need to sort a portion of a file in a Alphabetical Order.
Example : The user adam is not sorted and the user should get sorted. I don't want the complete file to get sorted.
Currently All_users.txt contains the following lines.
##############
# ARS USERS
##############
mike, Mike... (6 Replies)
I am trying to parse a file but the filehas binary data inline mixed with text fields.
I tried the binutils strings function , it get the binary data out but put the char following the binary data in a new line .
input file
app_id:1936 pgm_num:0 branch:TBNY ord_num:0500012(–QMK) deal_num:0... (12 Replies)
Hi,
I have a log file that gets updated every second. Currently the size has grown to 20+ GB. I need to have a command/script, that will try to get the actual size of the file and will remove 50% of the data that are in the log file. I don't mind removing the data as the size has grown to huge... (8 Replies)
Discussion started by: Souvik Patra
8 Replies
LEARN ABOUT DEBIAN
bio::alignio::fasta
Bio::AlignIO::fasta(3pm) User Contributed Perl Documentation Bio::AlignIO::fasta(3pm)NAME
Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from fasta flat file databases. This is for the fasta alignment format, not for
the FastA sequence analysis program. To process the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.
FEEDBACK
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
Peter Schattner
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln
Function: returns the next alignment in the stream.
Returns : Bio::Align::AlignI object - returns 0 on end of file
or on error
Args : -width => optional argument to specify the width sequence
will be written (60 chars by default)
See Bio::Align::AlignI
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
See Bio::Align::AlignI
_get_len
Title : _get_len
Usage :
Function: determine number of alphabetic chars
Returns : integer
Args : sequence string
width
Title : width
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::AlignIO::fasta(3pm)