version 1.0.0

artic-network · Nov 10, 2023 · 80d4f32 · 80d4f32
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diff --git a/.Rhistory b/.Rhistory
diff --git a/README.md b/README.md
@@ -6,11 +6,24 @@ This command-line interface (CLI) generates IDT input files from a 7-column prim
 
 The IDT Input File Generator CLI allows you to convert a primer bed file into IDT input files. IDT (Integrated DNA Technologies) is a company that provides custom DNA synthesis services. This tool automates the process of generating input files for ordering primers from IDT.
 
+## Installation
+
+#### From pip
+
+```pip instal bed2idt```
+
+#### From Poetry / source
+
+```git clone https://github.com/ChrisgKent/bed2idt```
+
+```poetry install && poetry build```
+
 ## Usage
 
 To use the CLI, run the following command:
 
-    python bed2idt/main.py [options] [command] [command-options]
+    bed2idt [options] [command] [command-options]
+
 
 ## Options
 
@@ -19,25 +32,30 @@ The CLI supports the following options:
 -   `-b, --bedfile`: Path to the primer bed file (required).
 -   `-o, --output`: The output location for the generated IDT input file(s) (default: `output.xlsx`).
 -   `plate` command:
-    -   `-s, --splitby`: Specifies whether the primers should be split across more than one plate. Valid options are `pool`, `ref`, or `none` (default: `pool`).
+    -   `-s, --splitby`: Specifies whether the primers should be split across more than one plate. Valid options are `pool`, `ref`, `none`, ~~`next`~~ (default: `pool`).
+    -   `-f, --fillby`: Specifies how the plates should be filled. Valid options are `rows` or `cols` (default: `rows`).
 -   `tube` command:
     -   `-s, --scale`: The concentration of the primers. Valid options are `25nm`, `100nm`, `250nm`, `1um`, `2um`, `5um`, `10um`, `4nmU`, `20nmU`, `PU`, or `25nmS` (default: `25nm`).
     -   `-p, --purification`: The purification method for the primers. Valid options are `STD`, `PAGE`, `HPLC`, `IEHPLC`, `RNASE`, `DUALHPLC`, or `PAGEHPLC` (default: `STD`).
 -   `--force`: Overrides the output directory if it already exists.
 
 ## Examples
 
-1.  Generate 96-well plate IDT input files for a primer bed file named `primers.bed` and save/overide the output as `output.xlsx`, split by pools:
+1.  Generate 96-well plate IDT input files for a primer bed file named `primer.bed` and save/overide the output as `output.xlsx`, split by pools:
+
+    ```bed2idt -b primer.bed --force plate --splitby pools```
+
+2.  Generate tube IDT input files for a primer bed file named `primer.bed`, save the output as `custom_output.xlsx`, and specify a purification method:
 
-    ```python bed2idt/main.py -b primers.bed --force plate --splitby pools```
+    ```bed2idt -b primer.bed -o custom_output.xlsx tube --purification PAGE```
 
-2.  Generate tube IDT input files for a primer bed file named `primers.bed`, save the output as `custom_output.xlsx`, and specify a purification method:
+3.  Generate IDT input files for a primer bed file named `primer.bed` without splitting the primers across multiple plates:
 
-    ```python bed2idt/main.py -b primers.bed -o custom_output.xlsx tube --purification PAGE```
+    ```bed2idt -b primer.bed plate --splitby none```
 
-3.  Generate IDT input files for a primer bed file named `primers.bed` without splitting the primers across multiple plates:
+4.  Generate IDT input files `primer.xlsx` for a primer.bed file named `primer.bed`, splitting the plate by pool, and filling plates by col:
 
-    ```python bed2idt/main.py -b primers.bed plate --splitby none```
+    ```bed2idt -b primer.bed -o primer.xlsx plate  --splitby pools --filllby cols```
 
 Note: Make sure to replace `python` with the appropriate command for running Python on your system.
 

diff --git a/bed2idt/__init__.py b/bed2idt/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.0.0"
diff --git a/bed2idt/__pycache__/__init__.cpython-310.pyc b/bed2idt/__pycache__/__init__.cpython-310.pyc
diff --git a/bed2idt/__pycache__/cli.cpython-310.pyc b/bed2idt/__pycache__/cli.cpython-310.pyc
diff --git a/bed2idt/__pycache__/main.cpython-310.pyc b/bed2idt/__pycache__/main.cpython-310.pyc
diff --git a/bed2idt/cli.py b/bed2idt/cli.py
@@ -1,10 +1,12 @@
 import argparse
 import pathlib
+from bed2idt.__init__ import __version__
 
 
 def cli():
     description = "Generates IDT input files from the 7 col primer.bed"
     parser = argparse.ArgumentParser(description=description)
+    parser.add_argument("--version", version=__version__, action="version")
     parser.add_argument(
         "-b",
         "--bedfile",
@@ -30,6 +32,13 @@ def cli():
         default="pool",
         help="Should the primers be split across more than one plate",
     )
+    plate_parser.add_argument(
+        "-f",
+        "--fillby",
+        choices=["rows", "cols"],
+        default="rows",
+        help="How should the plate be filled",
+    )
     # Add the tube arguments
     tube_parser = subparsers.add_parser("tube")
     tube_parser.add_argument(

diff --git a/bed2idt/main.py b/bed2idt/main.py
@@ -3,6 +3,8 @@
 import sys
 import xlsxwriter
 
+from bed2idt.__init__ import __version__
+
 """
 These are the correct values on the IDT website as of time of writing
 Please check https://eu.idtdna.com/site/order/oligoentry to confirm
@@ -15,12 +17,17 @@ def chunks(lst, n):
         yield lst[i : i + n]
 
 
-def create_plate(primer_list: list[list], workbook, sheet_name: str):
+def create_plate(primer_list: list[list], workbook, sheet_name: str, by_rows: bool):
     for index, primer_sublist in enumerate(primer_list):
         # Create all the indexes in a generator
         letters = ["A", "B", "C", "D", "E", "F", "G", "H"]
         numb = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
-        indexes = ((letter, str(number)) for letter in letters for number in numb)
+
+        # Ensure the plate is filled up correctly
+        if by_rows:
+            indexes = ((letter, str(number)) for letter in letters for number in numb)
+        else:
+            indexes = ((letter, str(number)) for number in numb for letter in letters)
 
         # Create the sheet
         worksheet = workbook.add_worksheet(f"{sheet_name}.{index}")
@@ -93,7 +100,12 @@ def plate(primer_list, workbook, args):
 
     for index, plate in enumerate(plates):
         if plate:  # Plates can be empty so only write non-empty plates
-            create_plate(plate, workbook, sheet_name=f"plate_{index +1}")
+            create_plate(
+                plate,
+                workbook,
+                sheet_name=f"plate_{index +1}",
+                by_rows=args.fillby == "rows",
+            )
 
     workbook.close()
 

diff --git a/dist/bed2idt-0.1.0-py3-none-any.whl b/dist/bed2idt-0.1.0-py3-none-any.whl
diff --git a/dist/bed2idt-0.1.0.tar.gz b/dist/bed2idt-0.1.0.tar.gz
diff --git a/dist/bed2idt-1.0.0-py3-none-any.whl b/dist/bed2idt-1.0.0-py3-none-any.whl
diff --git a/dist/bed2idt-1.0.0.tar.gz b/dist/bed2idt-1.0.0.tar.gz
diff --git a/nibcs_v2.0.1.xlsx b/nibcs_v2.0.1.xlsx
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bed2idt"
-version = "0.1.0"
+version = "1.0.0"
 description = "Converts primer.bed files to IDT ordering templates"
 authors = ["ChrisKent <[email protected]>"]
 license = "CC-BY-SA-4.0"

diff --git a/tests/__init_.py b/tests/__init_.py
diff --git a/tests/test_plates.py b/tests/test_plates.py