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::seqio::tab
Bio::SeqIO::tab(3pm) User Contributed Perl Documentation Bio::SeqIO::tab(3pm)NAME
Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id" "sequence"
"
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 tabbed flat file databases.
It is very useful when doing large scale stuff using the Unix command line utilities (grep, sort, awk, sed, split, you name it). Imagine
that you have a format converter 'seqconvert' along the following lines:
my $in = Bio::SeqIO->newFh(-fh => *STDIN , '-format' => $from);
my $out = Bio::SeqIO->newFh(-fh=> *STDOUT, '-format' => $to);
print $out $_ while <$in>;
then you can very easily filter sequence files for duplicates as:
$ seqconvert < foo.fa -from fasta -to tab | sort -u |
seqconvert -from tab -to fasta > foo-unique.fa
Or grep [-v] for certain sequences with:
$ seqconvert < foo.fa -from fasta -to tab | grep -v '^S[a-z]*control' |
seqconvert -from tab -to fasta > foo-without-controls.fa
Or chop up a huge file with sequences into smaller chunks with:
$ seqconvert < all.fa -from fasta -to tab | split -l 10 - chunk-
$ for i in chunk-*; do seqconvert -from tab -to fasta < $i > $i.fa; done
# (this creates files chunk-aa.fa, chunk-ab.fa, ..., each containing 10
# sequences)
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
Philip Lijnzaad, p.lijnzaad@med.uu.nl
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
Args :
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 : Bio::Seq object
perl v5.14.2 2012-03-02 Bio::SeqIO::tab(3pm)