Which I do not want.
So how can I add a "\n" before ">" and after "my lines"
how can read the next line and check if ">" occurs if so need to add "\n" to the end of current line.
Will awk be faster or PERL is the way to go as the file is huge. Thousands of line and more.
One of the programs in perl using arrays went out of memory ,
so need to read and print line by line rather than buffer first.
Thanks
Last edited by Franklin52; 03-19-2010 at 05:31 AM..
Reason: Please use code tags!
Hi,
I'm not very familiar with unix shell. I want to replace the combination of two carriage returns and one newline with one carriage return and one newline. I think the best way to do this is to use sed. I tried something like this:
sed -e "s#\#\#g" file.txt
but it doesn't work.
Thanx... (2 Replies)
I am trying to use sed to replace specific characters at a specific position in the file with a different value... can this be done?
Example:
File:
A0199999123
A0199999124
A0199999125
Need to replace 99999 in positions 3-7 with 88888.
Any help is appreciated. (5 Replies)
Greetings.
I don't have experience programing scripts. I need to insert a string in a specific position of another string on another file (last.cfg), for example:
File last.cfg before using script:
login_interval=1800
lcs.machinename=client04
File last.cfg after using script:... (4 Replies)
I want to remove text from nth position to nth position couple of times in same line
my line is
"hello is there anyone can help me with this question"
I need like this
ello is there anyone can help me with question
'h' is removed and 'this' removed from the line. I want to do this... (5 Replies)
I woud like to substitue a string on a specific position for specific lines
I've got a file and I would like to change a specific string from "TOCHANGE" to "ABCABCAB"
For every line (except 1,2, 3 and the last one) , I need to check between the 9th and the 16th digits.
For the 3rd line, I... (7 Replies)
Hi,
I have file with lines key=val.
For ex(conf.file):-
c=3
ef=78
b=40
ca=40
I want to remove the line with c=3, when I execute the below command it's removing both lines i.e c=3 and ca=40. Could you please correct my command.
/usr/xpg4/bin/awk -v key=c 'match($0,key)... (3 Replies)
I have a file that I need to parse using a script. The dates in the file are displayed in the format:
Mar 2, 2011 9:09:31 PM
I have tried using the date command %e and %l but it pads an extra space for the day and hour if they are single digits.
So this I used a normal date command:
... (6 Replies)
Hi Gurus,
Apologies as I feel like this must be answered already on here somewhere but I just can't find it. I find many people looking to remove all \n and \r (CR and LF) or one or the other but the only times I've found someone trying to remove them only when both are together they've found... (7 Replies)
Hi,
I have a fixed width file.
The way this file works is say for example there are 30 columns in it each with different sizes say 10,5,2, etc...
If data in a field is less than the field size the rest of it is loaded with spaces.
I would like an awk command to that would replace
I have... (8 Replies)
Hi,
I have a file like this (about 8 columns in total, this being the 2nd column)
gi_49482297_ref_YP_039521.1_
gi_49482297_ref_YP_039521.1_
gi_49482315_ref_YP_039539.1_
gi_49482315_ref_YP_039539.1_I want to remove the _ at the end of the line.
And at later stages I would want to replace the... (5 Replies)
Discussion started by: Syeda Sumayya
5 Replies
LEARN ABOUT DEBIAN
formatdb
FORMATDB(1) NCBI Tools User's Manual FORMATDB(1)NAME
formatdb - format protein or nucleotide databases for BLAST
SYNOPSIS
formatdb [-] [-B filename] [-F filename] [-L filename] [-T filename] [-V] [-a] [-b] [-e] [-i filename] [-l filename] [-n str] [-o] [-p F]
[-s] [-t str] [-v N]
DESCRIPTION
formatdb must be used in order to format protein or nucleotide source databases before these databases can be searched by blastall,
blastpgp or MegaBLAST. The source database may be in either FASTA or ASN.1 format. Although the FASTA format is most often used as input
to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source for other formats such as the GenBank
report. Once a source database file has been formatted by formatdb it is not needed by BLAST. Please note that if you are going to apply
periodic updates to your BLAST databases using fmerge(1), you will need to keep the source database file.
OPTIONS
A summary of options is included below.
- Print usage message
-B filename
Binary Gifile produced from the Gifile specified by -F. This option specifies the name of a binary GI list file. This option
should be used with the -F option. A text GI list may be specified with the -F option and the -B option will produce that GI list
in binary format. The binary file is smaller and BLAST does not need to convert it, so it can be read faster.
-F filename
Gifile (file containing list of gi's) for use with -B or -L
-L filename
Create an alias file named filename, limiting the sequences searched to those specified by -F.
-T filename
Set the taxonomy IDs in ASN.1 deflines according to the table in filename.
-V Verbose: check for non-unique string ids in the database
-a Input file is database in ASN.1 format (otherwise FASTA is expected)
-b ASN.1 database is binary (as opposed to ASCII text)
-e Input is a Seq-entry. A source ASN.1 database (either text ascii or binary) may contain a Bioseq-set or just one Bioseq. In the
latter case -e should be provided.
-i filename
Input file(s) for formatting
-l filename
Log file name (default = formatdb.log)
-n str Base name for BLAST files (defaults to the name of the original FASTA file)
-o Parse SeqID and create indexes. If the source database is in FASTA format, the database identifiers in the FASTA definition line
must follow the conventions of the FASTA Defline Format.
-p F Input is a nucleotide, not a protein.
-s Index only by accession, not by locus. This is especially useful for sequence sets like the EST's where the accession and locus
names are identical. Formatdb runs faster and produces smaller temporary files if this option is used. It is strongly recommended
for EST's, STS's, GSS's, and HTGS's.
-t str Title for database file [String]
-v N Break up large FASTA files into `volumes' of size N million letters (4000 by default). As part of the creation of a volume, for-
matdb writes a new type of BLAST database file, called an alias file, with the extension `nal' or `pal'.
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO blast(1), copymat(1), formatrpsdb(1), makemat(1), /usr/share/doc/blast2/formatdb.html.
NCBI 2007-10-19 FORMATDB(1)
03-18-2010
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