Skip to content

Commit

Permalink
updated docs to show changes in find_path
Browse files Browse the repository at this point in the history
  • Loading branch information
samarendra-pani committed Oct 8, 2024
1 parent e3e0a3f commit ad3920f
Showing 1 changed file with 5 additions and 4 deletions.
9 changes: 5 additions & 4 deletions docs/guide.rst
Original file line number Diff line number Diff line change
Expand Up @@ -42,24 +42,25 @@ This subcommand retrieves the base seqeunce of paths in the given GFA.
Usage
-----

The :code:`find_path` subcommand takes 2 obligatory inputs, a GFA file and node path (like :code:`">s82312<s82313"` (with the quotes)).
It returns the sequence of the path.
The :code:`find_path` subcommand takes 2 obligatory inputs, a GFA file and node path (like :code:`">s82312<s82313"` (with the quotes)) or file path which has node paths.
It returns the sequence of the path(s) by default but using the :code:`--fasta` flag, the sequences will be returned as a FASTA file.

.. code-block::
:caption: find_path arguments
usage: gaftools find_path [-h] [-o OUTPUT] GFA path
usage: gaftools find_path [-h] [-o OUTPUT] [-f] GFA path
Find the genomic sequence of a given GFA path.
positional arguments:
GFA Input GFA file (can be bgzip-compressed)
path GFA path to retrieve the sequence (e.g., ">s82312<s82313").
path GFA node path to retrieve the sequence (e.g., ">s82312<s82313") OR a filepath containing node paths in different lines
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
Output file. If omitted, use standard output.
-f, --fasta Flag to output the sequence as a FASTA file with the seqeunce named seq_<node path>
.. _gaftools-index:

Expand Down

0 comments on commit ad3920f

Please sign in to comment.