02-12-2020
Thank you so much, this works perfectly.
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Hi all,
I am working on a shell script to extract information from a file that has output from Oracle sqlplus. The problem is that the output of a single line is spread across multiple lines and i do not know as how to extract the particular filed at ones,which spans multiple lines.... (2 Replies)
Discussion started by: harris2107
2 Replies
2. Shell Programming and Scripting
Hi,
Following is sample portion of the file;
<JDBCConnectionPool DriverName="oracle.jdbc.OracleDriver"
MaxCapacity="10" Name="MyApp_DevPool"
PasswordEncrypted="{3DES}7tXFH69Xg1c="
Properties="user=MYAPP_ADMIN" ShrinkingEnabled="false"
... (12 Replies)
Discussion started by: sujoy101
12 Replies
3. UNIX for Dummies Questions & Answers
Hi
I need to put together a script that will search certain tables in a db and send that data to a csv file.
Basically I am importing data to a db and I want to write a script to check that all information was imported correctly.
Thank you (1 Reply)
Discussion started by: ladyAnne
1 Replies
4. Shell Programming and Scripting
Hi to all,
I got this content/pattern from file http.log.20110808.gz
mail1 httpd: Account Notice: close igchung@abc.com 2011/8/7 7:37:36 0:00:03 0 0 1
mail1 httpd: Account Information: login sastria9@abc.com proxy sid=gFp4DLm5HnU
mail1 httpd: Account Notice: close sastria9@abc.com... (16 Replies)
Discussion started by: Mr_47
16 Replies
5. Shell Programming and Scripting
Hi, i have a file like this:
<Iteration>
<Iteration_iter-num>3</Iteration_iter-num>
<Iteration_query-ID>lcl|3_0</Iteration_query-ID>
<Iteration_query-def>G383C4U01EQA0A length=197</Iteration_query-def>
<Iteration_query-len>197</Iteration_query-len>
... (9 Replies)
Discussion started by: the_simpsons
9 Replies
6. Shell Programming and Scripting
Hi,
I have a file which I need to programmatically split into two files.
All the information in the file before pattern "STOP HERE" is to be stripped and output into one file while everything after "STOP HERE" is to be output into a separate file.
I would appreciate help on how to do... (8 Replies)
Discussion started by: PTL
8 Replies
7. Shell Programming and Scripting
The below awk parser works for most data inputs, but I am having trouble with the last one. The problem is in the below rules steps 1 and 2 come from $2 (NC_000013.10:g.20763686_20763687delinsA) and steps 3 and 4 come from $1 (NM_004004.5:c.34_35delGGinsT).
Parse Rules:
The header is... (0 Replies)
Discussion started by: cmccabe
0 Replies
8. Shell Programming and Scripting
Gents,
If is possible please help.
I have a big file (example attached) which contends exactly same value in column, but from column 2 to 6 these values are diff. I will like to compile for all records all columns like the example attached in .csv format (output.rar ).. The last column in the... (11 Replies)
Discussion started by: jiam912
11 Replies
9. Shell Programming and Scripting
In a particular directory, there can be 1000 files like below.
filename is job901.ksh
#!/bin/ksh
cront -x << EOJ
submit file=$PRODPATH/scripts/genReport.sh maxdelay=30
&node=xnode01
tname=job901
&pfile1=/prod/mldata/data/test1.dat
... (17 Replies)
Discussion started by: vedanta
17 Replies
10. Shell Programming and Scripting
Hi all, I have a query that runs that outputs data in the following format -
01/09/12 11:43:40,ADMIN,4,77,Application Group Load: Name(TESTED) LoadId(5137-1-0-1XX-15343-15343) File(/dir/dir/File.T03.CI2.RYR.2012009.11433350806.ARD) InputSize(5344) OutputSize(1359) Rows(2) Time(1.9960)... (8 Replies)
Discussion started by: jeffs42885
8 Replies
LEARN ABOUT DEBIAN
bp_seqfeature_load
BP_SEQFEATURE_LOAD(1p) User Contributed Perl Documentation BP_SEQFEATURE_LOAD(1p)
NAME
bp_seqfeature_load.pl - Load GFF into a SeqFeature database
DESCRIPTION
Pass any number of GFF or fasta format files (or GFF with embedded fasta) to load the features and sequences into a SeqFeature database.
The database (and adaptor) to use is specified on the command line. Use the --create flag to create a new SeqFeature database.
SYNOPSIS
bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]]
Try 'bp_seqfeature_load.pl --help' or '--man' for more information.
OPTIONS
-d, --dsn
DBI data source (default dbi:mysql:test)
-n, --namespace
The table prefix to use (default undef) Allows several independent sequence feature databases to be stored in a single database
-s, --seqfeature
The type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature)
-a, --adaptor
The storage adaptor (class) to use (default DBI::mysql)
-v, --verbose
Turn on verbose progress reporting (default true) Use --noverbose to switch this off.
-f, --fast
Activate fast loading. (default 0) Only available for some adaptors.
-T, --temporary-directory
Specify temporary directory for fast loading (default File::Spec->tmpdir())
-i, --ignore-seqregion
If true, then ignore ##sequence-region directives in the GFF3 file (default, create a feature for each region)
-c, --create
Create the database and reinitialize it (default false) Note, this will erase previous database contents, if any.
-u, --user
User to connect to database as
-p, --password
Password to use to connect to database
-z, --zip
Compress database tables to save space (default false)
-S, --subfeatures
Turn on indexing of subfeatures (default true) Use --nosubfeatures to switch this off.
--summary
Generate summary statistics for coverage graphs (default false) This can be run on a previously loaded database or during the load. It
will default to true if --create is used.
--noalias-target
Don't create an Alias attribute whose value is the target_id in a Target attribute (if the feature contains a Target attribute, the
default is to create an Alias attribute whose value is the target_id in the Target attribute)
Please see http://www.sequenceontology.org/gff3.shtml for information about the GFF3 format. BioPerl extends the format slightly by adding
a ##index-subfeatures directive. Set this to a true value if you wish the database to be able to retrieve a feature's individual parts
(such as the exons of a transcript) independently of the top level feature:
##index-subfeatures 1
It is also possible to control the indexing of subfeatures on a case-by-case basis by adding "index=1" or "index=0" to the feature's
attribute list. This should only be used for subfeatures.
Subfeature indexing is true by default. Set to false(0) to save lots of database space and speed performance. You may use --nosubfeatures
to force this.
perl v5.14.2 2012-03-02 BP_SEQFEATURE_LOAD(1p)