You cannot use shell variables inside awk in that manner, which causes malfunctions. $i for instance would be, if i=1, field one, not a shell variable. You don't need the shell variable in the first place fortunately, awk can handle multiple files by itself.
This will create files 0001.out, 0002.out, etc, etc.
The name of the file currently being processed is available as the special varaible FILENAME, if you want to base the output filename on it.
Hi,
I have a file that looks like this (tab deliminited).
MAT1 YKR2 3
MAT1 YMR1 2
MAT1 YFG2 2
MAT2 YLM4 4
MAT2 YHL2 1
BAR1 YKR2 3
BAR1 YFR1 4
BAR1 YMR1 1
What I want to do is break this file down into multiple files. So the result will look like this:
File 1... (2 Replies)
Hi,
I have a code as given below
Set -A _Category="A\
B\
C"
for _cat in ${_Category}
do
sed -e "s:<TABLE_NAME>:${_cat}:g" \
-e "s:<date>:${_dt}:g" \
${_home}/skl/sq1.sql >> ${_dest}/del_${_dt}.sql
fi
... (4 Replies)
Hi.,
My current script extracts only if the date and time are in 3rd and 4th pos.
#!/bin/bash
echo "Enter the file name to extract the timestamp"
read fname
IFILE=$fname
F=$IFILE
IFS="_."
f=($F)
echo "Date ${f} Time ${f}"
How to generalize the script to extract the... (3 Replies)
Hello Friends,
I am trying to implement the following using UNIX. I am getting a sequential file as input which would have two columns, "Name" and "Countries Visited". The "Countries Visisted" field will be multi-valued, each value separated by a space and also the number of values are not... (2 Replies)
I've been trying to write a command-line function to grab a website's MX records and their ip addresses. The code below works with domains that only have one MX record:
function kmx { mx=`host -t MX $1 | awk '{ print $7 }'`;
ip=`host $mx | sed '/IPv6/d;/handled/d' | awk '{ print $4 }'`; ... (8 Replies)
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
Dear all,
I have huge txt file with the input files for some setup_code. However for running my setup_code, I require txt files with maximum of 1000 input files
Please help me in suggesting way to break down this big txt file to small txt file of 1000 entries only.
thanks and Greetings,
Emily (12 Replies)
I have the following data set about the snps ID txt file
POS ID
78599583 rs987435
33395779 rs345783
189807684 rs955894
33907909 rs6088791
75664046 rs11180435
218890658 rs17571465
127630276 rs17011450
90919465 rs6919430
and a gene... (7 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 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)