Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

bp_dbsplit(1p) [debian man page]

BP_DBSPLIT(1p)						User Contributed Perl Documentation					    BP_DBSPLIT(1p)

NAME
dbsplit - script to split an input set of database(s) into smaller pieces SYNOPSIS
dbsplit.PLS --size 50 [-i inputfile] [-if inputformat] [-of outputformat] [--prefix outputprefix] [ < file1 file 2 OR file1 file2] DESCRIPTION
This script will take as input a list of filenames or a single file or from STDIN a sequence database and split the database into separate files of X numbers of sequences. You specify X with the "--size/-s" parameter. The input and output sequence format is any that is supported by bioperl (fasta,embl,genbank,gcg, swissprot, etc). You can specify the input data either as a single file with -i filename, or as a single file as an argument like % dbsplit file1 file2 or as a list of sequence data with % cat file1 file2 file3 | dbsplit You'll want to use the "--prefix" to specify what the output prefix will be. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR
Jason Stajich, jason-at-bioperl-dot-org perl v5.14.2 2012-03-02 BP_DBSPLIT(1p)

Check Out this Related Man Page

BP_GCCALC(1p)						User Contributed Perl Documentation					     BP_GCCALC(1p)

NAME
gccalc - GC content of nucleotide sequences SYNOPSIS
gccalc [-f/--format FORMAT] [-h/--help] filename or gccalc [-f/--format FORMAT] < filename or gccalc [-f/--format FORMAT] -i filename DESCRIPTION
This scripts prints out the GC content for every nucleotide sequence from the input file. OPTIONS
The default sequence format is fasta. The sequence input can be provided using any of the three methods: unnamed argument gccalc filename named argument gccalc -i filename standard input gccalc < filename FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason@bioperl.org HISTORY
Based on script code (see bottom) submitted by cckim@stanford.edu Submitted as part of bioperl script project 2001/08/06 perl v5.14.2 2012-03-02 BP_GCCALC(1p)
Man Page

9 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Help finding/adding up file size...

Ok, I am new to UNIX and Shell scripting and I am trying to do the following using a korn shell script: I have a large data file that is loaded into a database, this data file is split into parts to make it more manageable based on a size parameter. The file contains many account records, the... (1 Reply)
Discussion started by: Stove13
1 Replies

2. Shell Programming and Scripting

how to call one script from another script...

Hi friends How to call another script file from running script i have file1.sh file ---------------- var= (file2.sh output) // file2.sh output will be in the i/p for var in file1.sh ------------------------ i need to call file2.sh here and that output should be input for file1.sh ... (2 Replies)
Discussion started by: kittusri9
2 Replies

3. UNIX for Dummies Questions & Answers

get the data in a file into single string

Hello everyone ! I need to get the data in a file into a string. file1 1 2 3 4 5 I need to write a script where the file1 info is stored in a string (say variable s). So the output should be 1,2,3,4,5 or (1,2,3,4,5) If i say echo $s or print $s output should be 1,2,3,4,5 or ... (7 Replies)
Discussion started by: i.scientist
7 Replies

4. Shell Programming and Scripting

how to write a script contain list of questions

hi i want to write a script that contain questions upto 50..when i run the script it has to ask the questions one by one with options like a,b,c,d and user has to answer the each question and finally result (contain how many user selected correctly) please help me...i need hints to do....... (8 Replies)
Discussion started by: srinivas2828
8 Replies

5. Shell Programming and Scripting

connecting to different database in sqr

Hi, My requirement is to generate a single text output which fetches data from two different databases. I have two different sqrs to generate text file1(data from db1) and file2(data from db2). can I execute both the sqrs from a single shell script? If yes, pls let me know how to connect to db2... (1 Reply)
Discussion started by: vimalr
1 Replies

6. Shell Programming and Scripting

Need script to take input from file, match on it in file 2 and input data

All, I am trying to figure out a script to run in windows that will allow me to match on First column in file1 to 8th Column in File2 then Insert file1 column2 to file2 column4 then create a new file. File1: 12345 Sam 12346 Bob 12347 Bill File2:... (1 Reply)
Discussion started by: darkoth
1 Replies

7. Shell Programming and Scripting

Parsing a fasta sequence with start and end coordinates

Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this? For Example Chr 1 is in following format I need regions from 2 - 10 should give me AATTCCAAA and in a similar way 15- 25 should give... (8 Replies)
Discussion started by: empyrean
8 Replies

8. Shell Programming and Scripting

Summing numbers after specific word

Hi all, Looking for suggestions on a better way to sum numbers in a key value pair formated file. What I have works but seems really clunky to me. Any suggestions would be greatly appreciated. cat test.txt | perl -ne 'm/(M=)(\d+\.?\d?\d?)/ && print "$2\n"' | awk '{ sum+=$1} END {printf... (7 Replies)
Discussion started by: cgol
7 Replies

9. Shell Programming and Scripting

How to read a file, line by line in UNIX script?

#!/bin/bash file1="yxd" for file in `cat file3.txt`; do cat $file1 | awk '{split($1,dp,"."); lend=length(dp); if(lend>2) { dom=dp"."dp; split($2,ipl,","); for(i=1; i<=length(ipl); i++) { if(ipl~/:/) { if(ipl~/:/) i++; rip=ipl; i++; raq=ipl; rtq=0; si=i+4; for(;i<si;i++) rtq+=ipl; rsub="";... (2 Replies)
Discussion started by: veeruasu
2 Replies

Featured Tech Videos