Input file:
Desired output:
Once the program find "pir||"
I hope to replace "pir||" into "pir|' and follow by replace the next shown "_" into "|"
Command I try:
I just able to replace the "pir||" into "pir|' but I don't know how to replace the following "_" into "|"
Thanks for any advice.
I am trying to write an awk program to reformat a data table and convert the date to julian time. I have all the individual steps working, but I am having some issues joing them into one program. Can anyone help me out? Here is my code so far:
# This is an awk program to convert the dates from... (4 Replies)
I am new to Perl. I need to reformat a data file as the last part of a script I am working on. I am stuck on this.
Here is the current format:
CUSTOMER Filename 09/04/07-08:49
CUSTOMER Filename 09/04/07-08:52
CUSTOMER Filename 09/04/07-08:52
CUSTOMER2 Filename 09/04/07-08:49
CUSTOMER2... (3 Replies)
Can anyone help me with a shell script that can do the following:
I have a data in fasta format (first line is the header, followed by a sequence of characters).
>ALLLY
GGCCCCTCGAGCCTCGAACCGGAACCTCCAAATCCGAGACGCTCTGCTTATGAGGACCTC
GAAATATGCCGGCCAGTGAAAAAATCTTGTGGCTTTGAGGGCTTTTGGTTGGCCAGGGGC... (5 Replies)
I have a file which have data like
A.txt
a
1Jan I am in a1.
1Jan I was born.
2Jan I am here.
3Jan I am in a3.
b
1Jan I am in b1.
c
2Jan I am in c2.
d
2Jan I am in d2.
5jan I am in d5.
date in the file might be vary evertime. (9 Replies)
Hi,
I am writing just to share my appreciation for help I have received from this site in the past.
In a previous post Split File by Data Group I received a lot of help with a troublesome awk script to reformat some complicated data blocks. What I learned really came in hand recently when I... (1 Reply)
I am helping my wife set up a real estate site and I am starting to integrate MLS listings. We are using a HostGator level 5 VPS running CentOS and have full root and SSH access to the VPS.
Thus far I have automated the daily FTP download of listings from our MLS server using a little sh script.... (4 Replies)
sindex(1) Biosquid Manual sindex(1)NAME
sindex - index a sequence database for sfetch
SYNOPSIS
sindex [options] seqfile1 [seqfile2...]
DESCRIPTION
sindex indexes one or more seqfiles for future sequence retrievals by sfetch. An SSI ("squid sequence index") file is created in the same
directory with the sequence files. By default, this file is called <seqfile>.ssi.
If there is more than one sequence file on the command line, the SSI filename will be constructed from the last sequence file name. This
may not be what you want; see the -o option to specify your own name for the SSI file.
sindex is capable of indexing large files (>2 GB) if optional LFS support has been enabled at compile-time. See INSTALL instructions that
came with @PACKAGE@.
OPTIONS -h Print brief help; includes version number and summary of all options, including expert options.
-o <ssi outfile>
Direct the SSI index to a file named <outfile>. By default, the SSI file would go to <seqfile>.ssi.
EXPERT OPTIONS --64 Force the SSI file into 64-bit (large seqfile) mode, even if the seqfile is small. You don't want to do this unless you're debug-
ging.
--external
Force sindex to do its record sorting by external (on-disk) sorting. This is only useful for debugging, too.
--informat <s>
Specify that the sequence file is definitely in format <s>; blocks sequence file format autodetection. This is useful in automated
pipelines, because it improves robustness (autodetection can occasionally go wrong on a perversely misformed file). Common examples
include genbank, embl, gcg, pir, stockholm, clustal, msf, or phylip; see the printed documentation for a complete list of accepted
format names.
--pfamseq
A hack for Pfam; indexes a FASTA file that is known to have identifier lines in format ">[name] [accession] [optional description]".
Normally only the sequence name would be indexed as a primary key in a FASTA SSI file, but this allows indexing both the name (as a
primary key) and accession (as a secondary key).
SEE ALSO afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sreformat(1), strans-
late(1), weight(1).
AUTHOR
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU
General Public License (GPL) See COPYING in the source code distribution for more details, or contact me.
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX : 1-314-362-2157
Email: eddy@genetics.wustl.edu
Biosquid 1.9g January 2003 sindex(1)