coalispr.resources.share.get_smallRNAs_and_targets

Scripts for collecting small RNA info and putative targets from input.

Functions

create_gtfs(kind, get_all, targets, library, ...)

Create a GTF file for kind of RNA from infile, using reference if needed

main(args)

Module Contents

coalispr.resources.share.get_smallRNAs_and_targets.create_gtfs(kind, get_all, targets, library, reference, outname)

Create a GTF file for kind of RNA from infile, using reference if needed

Parameters:

  • kind (str) – Kind of RNA the GTF is made for, like ‘miRNA’.

  • get_all (int) – Flag to indicate to get 0: minimal (i.e. only displayed by coalispr showgraphs) or 1: all annotations for a feature

  • targets (str) – Name for input file with ids for genes to be annotated

  • library (str) – Name for file with info for gene ID conversions

  • reference (str) – Name for gtf with all genome annotations to be mined as reference

  • otname (str) – Name for output file

Returns:

An annotation file with the following fields:

seqname  - The name of the sequence. Must be a chromosome or
           scaffold.
source   - The program that generated this feature.
feature  - The name of this type of feature. Some examples of
           standard feature types are "CDS", "start_codon",
           "stop_codon", and "exon".
start    - The starting position of the feature in the
           sequence. The first base is numbered 1.
end      - The ending position of the feature (inclusive).
score    - A score between 0 and 1000. If the track line
           useScore attribute is set to 1 for this annotation
           data set, the score value will determine the level
           of gray in which this feature is displayed (higher
           numbers = darker gray). If there is no score value,
           enter ".".
strand   - Valid entries include '+', '-', or '.' (for don't
           know/don't care).
frame    - If the feature is a coding exon, frame should be a
           number between 0-2 that represents the reading
           frame of the first base. If the feature is not a
           coding exon, the value should be '.'.
comments - gene_id "Em:U62317.C22.6.mRNA"; transcript_id
           "Em:U62317.C22.6.mRNA"; exon_number 1

Return type:

GTF file

coalispr.resources.share.get_smallRNAs_and_targets.main(args)