File_Select v1.0

Owned by upendra kumar Devisetty
Last updated: Dec 21, 2018
1 min read

The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the documentation and add your comments on the bottom of this page, or email comments to support@cyverse.org.

Rationale and background:


Splitting a large file into a number of small lines based on line number is essential for many applications or analysis. This is especially useful if you have a long list of id's and then you want to use them parallelly using HT Analysis Path List file.

Pre-Requisites:

A CyVerse account (Register for a CyVerse account at https://user.cyverse.org).

An up-to-date Java-enabled web browser. (Firefox recommended. If you wish to work with your own large datasets and upload them using iCommands, Chrome is not suitable due to its issues in utilizing 64-bit Java.)

Mandatory arguments

  1. Inputs
    1. Input File: Path to the input file that contains the list of id's
    2. Number of lines per file: How many lines that you want to split the input file into. The number of output files corresponds tonumberof lines that you want to split into
    3. File_prefix: Prefix of the file that gets created (Default is "x")
  2. Outputs
    1. Output folder: Name of the output folder (Default is "Output")

Test run

The test data for this app is located at /iplant/home/shared/iplantcollaborative/example_data/OSG-RMTA/sra_id_list.txt
The 'sra_id_list.txt' file contains a list of 15 SRA id's, one SRA ID per line

 

SRR3403881
SRR5227388
SRR5227389
SRR5227390
SRR5227391
SRR5227392
SRR5227393
SRR5227394
SRR5227395
SRR5227396
SRR5227397
SRR5227398
SRR5227399
SRR5227400
SRR5227401
  1. Inputs
    1. Input File: /iplant/home/shared/iplantcollaborative/example_data/OSG-RMTA/sra_id_list.txt
    2. Number of lines per file: 5
    3. File_prefix: osg_rmta_
  2. Outputs
    1. Output folder: OSG-RMTA-File-Split

After a successful run, you'll get 3 files each containing 5 SRA Id's with the prefix osg_rmta_ in OSG-RMTA-File-Split folder