goatools.cli.wr_hierarchy module

Command-line script to print a GO term's lower-level hierarchy.

Usage:
  goatools wr_hier [GO ...] [options]

Options:
  -h --help      show this help message and exit

  -i <gofile.txt>  Read a file name containing a list of GO IDs
  -o <outfile>     Output file in ASCII text format
  -f               Writes results to an ASCII file named after the GO term. e.g. hier_GO0002376.txt
  --up             Write report from GO term up to root

  --dag=<dag_file>    Ontologies in obo file [default: go-basic.obo].

  --gaf=<file.gaf>    Annotations from a gaf file
  --gene2go=<gene2go> Annotations from a gene2go file downloaded from NCBI
  --taxid=<Taxonomy_number> Taxid is required is using gene2go

  --no_indent         Do not indent GO terms
  --max_indent=<int>  max indent depth for printing relative to GO Term
  --concise           If a branch has already been printed, do not re-print.
                      Print '===' instead of dashes to note the point of compression
  --dash_len=<int>    Printed width of the dashes column [default: 6]
  --item_marks=<GOs>    GO IDs to be marked
  --include_only=<GOs>  GO IDs to be included with all others omitted
  -r --relationship   Load and use the 'relationship' field

goatools.cli.wr_hierarchy.cli(args=None)

Command-line script to print a GO term’s lower-level hierarchy.

goatools.cli.wr_hierarchy.main(args=None)

Print a GO term hierarchy from the command line.

class goatools.cli.wr_hierarchy.WrHierCli(args=None, prt=sys.stdout)

Bases: object

Write hierarchy cli.

kws_set_all = {'f', 'relationship', 'up'}

kws_dct_all = {'GO', 'concise', 'dag', 'dash_len', 'gaf', 'gene2go', 'i', 'include_only', 'item_marks', 'max_indent', 'no_indent', 'o', 'taxid'}

kws_dct_wr = {'concise', 'dash_len', 'max_indent', 'no_indent', 'relationship'}

static init_goids(goids_args, infile, go2nt)

Extract GO IDs in the report from arguments

get_fouts()

Get output filename.

wrtxt_hier(fout_txt)

Write hierarchy below specfied GO IDs to an ASCII file.

prt_hier(prt=sys.stdout)

Write hierarchy below specfied GO IDs.