add docs

endast · Nov 21, 2023 · ea48280 · ea48280
1 parent 1452723
commit ea48280
Show file tree

Hide file tree

Showing 2 changed files with 108 additions and 0 deletions.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -9,8 +9,15 @@ Welcome to fake-vcf's documentation!
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
+     usage
+     api
 
 
+.. note::
+
+   This project is under active development.
+
+Contents
 
 Indices and tables
 ==================

diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -0,0 +1,101 @@
+Usage
+=====
+
+.. _installation:
+
+Installation
+------------
+
+To use Lumache, first install it using pip:
+
+.. code-block:: shell
+
+    git clone https://github.com/endast/fake-vcf.git
+    cd fake-vcf
+    make poetry-download
+    make install
+
+Running
+----------------
+
+
+By default `fake-vcf` writes to stdout
+
+.. code-block::
+
+  poetry run fake-vcf -s 2 -r 2
+  ##fileformat=VCFv4.2
+  ##source=VCFake 0.1.0
+  ##FILTER=<ID=PASS,Description="All filters passed">
+  ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+  ##contig=<ID=chr1>
+  ##reference=ftp://ftp.example.com/sample.fa
+  ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1)">
+  ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+  ##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype">
+  #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S0000001	S0000002
+  chr1	63	rs143	C	A	96	PASS	DP=10;AF=0.5;NS=2	GT	0|0	0|0
+  chr1	71	rs31	A	T	37	PASS	DP=10;AF=0.5;NS=2	GT	0|0	0|0
+
+
+
+You can write to a vcf file by piping the output to a file:
+
+.. code-block:: shell
+
+  poetry run fake-vcf -s 2 -r 2 > fake_file.vcf
+  ls -lah
+  total 1
+  -rw-r--r--   1 magnus  staff   682B Jul 28 16:48 fake_file.vcf
+
+Or let the script write to a file directly using `-o`:
+
+.. code-block:: shell
+
+  poetry run fake-vcf -s 2 -r 2 -o fake_file.vcf
+
+  Writing to file fake_file.vcf
+  (No compression)
+  100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 50942.96it/s]
+  Done, data written to fake_file.vcf
+  ls -lah
+  total 1
+  -rw-r--r--   1 magnus  staff   682B Jul 28 16:48 fake_file.vcf
+
+
+And if you want the file gzipped add .gz to the file name:
+
+.. code-block:: shell
+
+  poetry run fake-vcf -s 2 -r 2 -o fake_file.vcf.gz
+
+  Writing to file fake_file.vcf
+  (No compression)
+  100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 50942.96it/s]
+  Done, data written to fake_file.vcf
+  ls -lah
+  total 2
+  -rw-r--r--   1 magnus  staff   682B Jul 28 16:56 fake_file.vcf
+  -rw-r--r--   1 magnus  staff   436B Jul 28 16:57 fake_file.vcf.gz
+
+
+
+To see all options use --help
+
+.. code-block:: shell
+
+    poetry run fake-vcf --help
+
+   Usage: fake-vcf [OPTIONS]
+
+  ╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+  │ --fake_vcf_path  -o                 PATH     Path to fake vcf file. If the path ends with .gz the file will be gzipped. [default: None]                                                                                                                                                                            │
+  │ --num_rows       -r                 INTEGER  Nr rows to generate (variants) [default: 10]                                                                                                                                                                                                                          │
+  │ --num_samples    -s                 INTEGER  Nr of num_samples to generate. [default: 10]                                                                                                                                                                                                                          │
+  │ --chromosome     -c                 TEXT     chromosome default chr1 [default: chr1]                                                                                                                                                                                                                               │
+  │ --seed                              INTEGER  Random seed to use [default: 42]                                                                                                                                                                                                                                      │
+  │ --sample_prefix  -p                 TEXT     Sample prefix ex: SAM =>  SAM0000001    SAM0000002 [default: S]                                                                                                                                                                                                       │
+  │ --phased             --no-phased             Simulate phased [default: phased]                                                                                                                                                                                                                                     │
+  │ --version        -v                          Prints the version of the fake-vcf package.                                                                                                                                                                                                                           │
+  │ --help                                       Show this message and exit.                                                                                                                                                                                                                                           │
+  ╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯