Command-line scripts
====================

:data:`plastid` includes the following command-line scripts. Click on a name below for more information:

   =========================   =============================================================================
   **Analysis of sequencing or quantitative data**                 
   ---------------------------------------------------------------------------------------------------------
   |counts_in_region|           Count the number of :term:`read alignments <alignment>` covering
                                arbitrary regions of interest in the genome, and calculate
                                read densities (in reads per nucleotide and in :term:`RPKM`)
                                over these regions
   
   |cs|                         Count the number of :term:`read alignments<alignment>`
                                and calculate read densities (in :term:`RPKM`)
                                specifically for genes and sub-regions (5' UTR,
                                CDS, 3' UTR)

   |get_count_vectors|          Fetch vectors of :term:`counts` or other quantitative data
                                at each nucleotide position
                                in one or more regions of interest, saving each vector
                                as its own line-delimited text file
                            
   |make_wiggle|                Create `wiggle`_ or `bedGraph`_ files from alignment files
                                after applying a read :term:`mapping rule` (e.g.
                                to map :term:`ribosome-protected footprints <footprint>`
                                at their :term:`P-sites <P-site offset>`), for
                                visualization in a :term:`genome browser`
                            
   |metagene|                   Compute a :term:`metagene` profile of :term:`read alignments`,
                                :term:`counts`, or quantitative data over one or more regions of interest,
                                optionally applying a :term:`mapping rule`
                            
   |phase_by_size|              Estimate :term:`sub-codon phasing` in
                                :term:`ribosome profiling` data
   
   |psite|                      Estimate position of ribosomal P-site within
                                :term:`ribosome profiling` :term:`read alignments`
                                as a function of read length
   -------------------------   -----------------------------------------------------------------------------
   **Generating or modifying genome annotations**    
   ---------------------------------------------------------------------------------------------------------
   |crossmap|                   Generate a :term:`mask file` annotating regions of the genome
                                that fail to produce
                                uniquely mapping reads under various alignment
                                criteria, so that they may be excluded from future analyses
                            
   |gff_parent_types|           Examine parent-child relationships of features
                                in a `GFF3`_ file
                            
   |reformat_transcripts|       Convert transcripts between `BED`_, `BigBed`_,
                                `GTF2`_, `GFF3`_, and `PSL`_ formats
                            
   |findjuncs|                  Find all unique splice junctions in one or more
                                transcript annotations, and optionally export these
                                in `Tophat`_'s ``.juncs`` format
                            
   |slidejuncs|                 Compare splice junctions discovered in data to those
                                in an annotation of known splice junctions, and,
                                if possible with equal sequence support, slide
                                discovered junctions to compatible known junctions.
   =========================   =============================================================================
