I am new to the world of UNIX scripting - and would like to make the following script:
I have 100 files numbered 1-100. However - i would like to continue the file list - so that I add another 100 files following on, so that file 101 = 99; file 102 = 98 ; 103 = 97 and so on....
(basically ...... (6 Replies)
Hi,
I am a beginner in awk scripting! I need your help; I want to replace the fifth column number (which is 15 here) here in this file for example :
ATOM 142 N PRO A 15
ATOM 143 CD PRO A 15
ATOM 144 HD1 PRO A 15
ATOM ... (5 Replies)
I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this:
> Seq I
ACGACTAGACGATAGACGATAGA
> Seq 2
ACGATGACGTAGCAGT
> Seq 3
ACGATACGAT
I know I can extract the IDs alone with the following code
grep... (3 Replies)
Hi All
I have a folder that contains hundreds of file with a names
3.msa
4.msa
21.msa
6.msa
345.msa
456.msa
98.msa
...
...
...
I need rename each of this file by adding "core_" in the begiining of each file such as
core_3.msa
core_4.msa
core_21.msa (4 Replies)
Hi All,
I have 100 files named - rep-0.txt, rep-2.txt...rep-99.txt.
They each contain information in the following format:
abc 1 qwe
asd 2 zxc
poi 3 lkj
pdh 4 ldf
hgf 5 tyu
i would like to re-number , so that all the new files (rep0.dat, rep1,dat....) have... (1 Reply)
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
I am new to the world of Linux scripting, and would like to make the following 2 scripts:
I have 67 files named Alk-0001.txt to Alk-0067.txt
I would like them to be numbered Alk-002.txt to Alk-0134.txt
eg
Alk-0001.txt > Alk-0002.txt
Alk-0002.txt > Alk-0004.txt
Alk-0003.txt > Alk-0006.txt
... (3 Replies)
Hi,
In sftp script to get files, I have to rename all the files which I am picking. Rename command does not work here. Is there any way to do this?
I am using #!/bin/ksh
For eg: sftp user@host <<EOF
cd /path
get *.txt
rename *.txt *.txt.done
... (7 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)
Discussion started by: dineshkumarsrk
11 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)