09-13-2013
+ one or more hit
* 0 or more hit
? 0 or 1 hit
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1. Shell Programming and Scripting
Dear friends
I am new to linux and was trying to split some files userwise in our linux server.
I have a data file of 156 continuous columns named ecscr final.
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Hi,
I have a log file which contains lines like below:
2010-07-19 07:13:19,021 ERROR system ...(text)
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3. Shell Programming and Scripting
Hi All,
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Hi All,
I am trying to find numbers with balance greater than 1 and less than equal 2 from the below file using awk
Input file
num ,bal
100199,1.708
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100232,2
output file
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5. Shell Programming and Scripting
Hello Guyz
I have been following this forum for a while and the solutions provided are super useful. I currently have a scenario where i need to search for a pattern and start searching by keeping the first pattern as a baseline
ABC
DEF
LMN
EFG
HIJ
LMN
OPQ
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6. Shell Programming and Scripting
Hi,
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In file, we have millions of records each of 1000 in length. And at specific position say 800 there is a space, we need to replace it with Character X if the ID in that row starts with 123.
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8. Shell Programming and Scripting
Input data as below (filetest.txt):
1|22 JAN Minimum Bal 20.00 | SAT
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I have this fileA
TEST FILE ABC
this file contains ABC;
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TEST FILE 123
this file contains ABC,
this file contains DEF,
this file contains XYZ,
this file contains KLM
;
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10. Shell Programming and Scripting
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LEARN ABOUT DEBIAN
bp_mask_by_search
BP_MASK_BY_SEARCH(1p) User Contributed Perl Documentation BP_MASK_BY_SEARCH(1p)
NAME
mask_by_search - mask sequence(s) based on its alignment results
SYNOPSIS
mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa
DESCRIPTION
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which
you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've
provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence specify the -t/--type
query flag.
This is going to read in the whole sequence file into memory so for large genomes this may fall over. I'm using DB_File to prevent keeping
everything in memory, one solution is to split the genome into pieces (BEFORE you run the DB search though, you want to use the exact file
you BLASTed with as input to this program).
Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta
By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string'
Options:
-f/--format=s Search report format (fasta,blast,axt,hmmer,etc)
-sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot)
--hardmask (booelean) Hard mask the sequence
with the maskchar [default is lowercase mask]
--maskchar=c Character to mask with [default is N], change
to 'X' for protein sequences
-e/--evalue=n Evalue cutoff for HSPs and Hits, only
mask sequence if alignment has specified evalue
or better
-o/--out/
--outfile=file Output file to save the masked sequence to.
-t/--type=s Alignment seq type you want to mask, the
'hit' or the 'query' sequence. [default is 'hit']
--minlen=n Minimum length of an HSP for it to be used
in masking [default 0]
-h/--help See this help information
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
perl v5.14.2 2012-03-02 BP_MASK_BY_SEARCH(1p)