Many of the database access scripts generate tab-delimited outputs that are convenient for further command-line processing or import into spreadsheets.
The code uses the Boost library for command-line argument processing, advanced file operations and REgular EXpression (regex) parsing.
The main Perl program, seq_router.pl, processes command line parameters and calls sequence analysis, domain boundary detection, and domain-processing modules for individual protein sequences.
However, it provides no graphical user interface and specialist user input is required (i.e. file formatting, syntactic restrictions, pre/post-processing through command line etc).
Command line interface 2. No parallel processing 3.
With the natural parallel processing of command line pipes plus the divide and conquer feature of sdfMultiplexer.pl, it took a few hours of computing time to process multiple libraries.
For batch processing, an additional command line interface is available; output can be provided in various formats, amongst them gif, ps, svg and pdf.
The least experienced user can steer the processing by a simple command line where little or no parameters must be set.
The core component is the NextClip command line tool, an efficient C program for processing mate pair FASTQ files, generating summary statistics and preparing reads for use in scaffolding.
Command line mode allows applying all data pre-processing steps, including double-centering and network smoothing, saving the resulting network layout as a XGMML file and saving the eigenvector decomposition of the Laplacian of the network graph for future use.
The GUI workflow follows the processing pipeline of the GiA Roots command line tool.
