upload of initial version of Python script and first README version

README.md

@@ -1 +1,14 @@
-# generate-stickers-AveryL7871
+# generate-stickers-AveryL7871
+
+This script reads sample names from a txt file (one name per line) and arranges them on a sheet of A4 paper so that they can be printed on Avery-Zweckform L7871 labels. The current version of the script is written in Python and is conceptually based on v1, which was written in bash.
+
+## Requirements
+- A UNIX type console (e.g. Terminal on macOS)
+- Python 3.5 or higher (e.g. Python 3.9.1 from https://www.python.org/downloads/mac-osx/ or Python 3.8.5 as it comes with the latest Anaconda release https://www.anaconda.com/products/individual)
+- LaTeX (e.g. TeX Live/MacTeX for macOS or any other TeX distribution, https://tug.org/mactex/)
+
+## How to use
+1. Put the script (generateStickers.py) in the folder that you want the output pdf to be in.
+2. Navigate to this folder using the command line: cd path/to/your/folder
+3. Run the script with: python3 generateStickers.py
+4. Follow the instructions that appear in the console.

generateStickers.py

@@ -0,0 +1,304 @@
+""" Version 2.0 dated 24th Feb 2021 by Gleb Ebert
+
+    This script reads sample names from a list, presents the user with
+    a couple of options to modify the names and arranges them on a
+    sheet of A4 paper so that it can be printed on Avery-Zweckform
+    L7871 labels
+"""
+
+from pathlib import Path # we use this for file path operations
+import subprocess # this is for passing commands to unix shell
+
+# create class with objects to format console output
+class color:
+    PURPLE = "\033[95m"
+    CYAN = "\033[96m"
+    DARKCYAN = "\033[36m"
+    BLUE = "\033[94m"
+    GREEN = "\033[92m"
+    YELLOW = "\033[93m"
+    RED = "\033[91m"
+    BOLD = "\033[1m"
+    UNDERLINE = "\033[4m"
+    END = "\033[0m"
+
+#######################################################################
+# This section deals with the initial input of sample names.
+#######################################################################
+
+# keep asking for file names until file exists or user aborts script
+while True:
+    # get input file name from user and store its name in variable
+    input_file = input(f"{color.BOLD + color.DARKCYAN}"
+        "Enter the name of the txt file containing your strain/isolate names "
+        f"(one per line) followed by [ENTER] to confirm: {color.END}")
+
+    # check if user input includes ".txt" suffix and add it if absent
+    if not input_file.endswith(".txt"):
+        input_file += ".txt"
+
+    # if file does not exist, print error message and exit script
+    if not Path(input_file).exists():
+        print(f"\n{color.BOLD + color.RED}File {input_file} not found. "
+              "Make sure file is present in your working directory:\n"
+              f"{Path().cwd()}\n"
+              "To change your working directory type "
+              f"'cd /Path/to/your/directory' then hit [ENTER]{color.END}")
+
+        # ask user whether he wants to type the file name again
+        input_file_again = input(f"{color.BOLD + color.DARKCYAN}"
+            "Do you want to type the file name again? "
+            f"Type \"yes\" or \"no\": \n{color.END}")
+
+        # if user wants to try again, restart loop
+        # otherwise exit script
+        if input_file_again.casefold() == "yes".casefold():
+            continue
+        else:
+            quit()
+    else:
+        break
+
+# open file in read mode
+with open(input_file, "r") as file_handle:
+    # convert file contents into a list
+    names_list_original = file_handle.read().splitlines()
+
+names_number = len(names_list_original) # get number of names
+
+# print some of the sample names
+print(f"\n{color.BOLD + color.DARKCYAN}"
+    f"Your file contains {names_number} names:\n{names_list_original[0]}, "
+    f"{names_list_original[1]} ... {names_list_original[-1]}{color.END}")
+
+# ask user whether he wants to type the file name again
+input_file_ok = input(f"{color.BOLD + color.DARKCYAN}Do you want to continue "
+    f"with these names? Type \"yes\" or \"no\": {color.END}")
+
+# exit script if user says no, otherwise continue
+if input_file_ok.casefold() == "no".casefold():
+    quit()
+
+# query user on output file name
+output_file_name = input(f"\n{color.BOLD + color.DARKCYAN}"
+    f"\nType the name of your output file without suffix: {color.END}")
+
+# check if user input includes ".txt" suffix and add it if not
+if not output_file_name.endswith(".txt"):
+   output_file_name += ".txt"
+
+# remove old output file and ignore error if it does not exist
+try:
+    output_file_path = Path(str(Path().absolute()) + "/" + output_file_name)
+    output_file_path.unlink()
+except (FileNotFoundError):
+    pass
+
+#######################################################################
+# The following section deals with name suffixes
+#######################################################################
+
+# give user choice whether to add suffixes
+input_suffix_if = input(f"\n{color.BOLD + color.DARKCYAN}"
+    "\nDo you want to add suffixes to your sample names? "
+    f"Type \"yes\" or \"no\": {color.END}")
+
+if input_suffix_if.casefold() == "yes".casefold():
+    # print explanation of inner workings once before continuing
+    print(f"\n{color.BOLD + color.DARKCYAN}"
+        "\n==========================================")
+    print("\nIn the following part of the script you will supply groups of "
+        "suffixes (e.g. treatment names or replicate numbers) separated by "
+        "spaces: \"CTRL TREAT1 TREAT2 TREAT3\". Each suffix will be combined "
+        "with each sample name (e.g. Strain1-TREAT1, Strain1-TREAT2 ... "
+        "Strain10-TREAT3). You will also have to opportunity to supply "
+        "multiple suffix groups one after the other (the result of this would "
+        "be something like Strain1-TREAT1-Replicate1, "
+        "Strain1-TREAT1-Replicate2 ...).{color.END}")
+
+    # initiate list with names to be modified
+    names_list_old = names_list_original
+
+    # Keep asking for suffixes and adding them to sample names
+    # until user stops loop.
+    while True:
+        # ask for group of suffixes
+        input_suffix_group = input(f"{color.BOLD + color.DARKCYAN}"
+            f"\nEnter a group of suffixes: {color.END}")
+
+        # split input into list of words
+        input_suffixes = input_suffix_group.split()
+
+        # reinitiate list so it is empty
+        names_list_new = []
+
+        # loop through all names and add each suffix
+        for name in names_list_old:
+            for suffix in input_suffixes:
+                names_list_new.append(name + "-" + suffix)
+
+        # replace old with new list
+        names_list_old = names_list_new
+
+        # ask user whether to run through another interation of the
+        # suffix loop
+        input_suffix_continue = input(f"\n{color.BOLD + color.DARKCYAN}"
+            "\nDo you want to add another group of suffixes? "
+            f"Type \"yes\" or \"no\": {color.END}")
+
+        # if user answers anything other than yes break out of loop,
+        # otherwise repeat
+        if input_suffix_continue.casefold() != "yes".casefold():
+            break
+        else:
+            continue
+
+    # Create output file in append mode, loop through latest list with
+    # modified names and write each one to a new line in the file.
+    with open(output_file_path, "a+") as sampleFile:
+        for item in names_list_new:
+            sampleFile.write(f"{item}\n")
+else:
+    names_list_new = names_list_original
+
+#######################################################################
+# logic and parameters for LaTeX typesetting
+#######################################################################
+
+# give user choice whether to print month and year
+input_date_if = input(f"\n{color.BOLD + color.DARKCYAN}"
+    "\nDo you want to print the current month and year on the stickers? "
+    f"Type \"yes\" or \"no\":  {color.END}")
+
+# give user choice whether to print month and year
+input_date_format = input(f"\n{color.BOLD + color.DARKCYAN}"
+    "\nDo you want the date to include the day in addition to month and year?"
+    f" Type \"yes\" or \"no\":  {color.END}")
+
+if input_date_format.casefold() == "yes".casefold():
+    latex_date = "\t\t\\DTMtwodigits{##3}-\\DTMtwodigits{##2}-##1"
+else:
+    latex_date = "\t\t\\DTMtwodigits{##2}-##1"
+
+# function that returns sticker content
+def return_sticker(x):
+    sticker = names_list_new[x].replace("_", "\_")
+    if len(sticker) >= 16:
+        sticker = "{\\ssmall " + sticker + "}"
+    if input_date_if.casefold() == "yes".casefold():
+        sticker = sticker + " \\mbox{\\DATE}"
+    else:
+        sticker = sticker + "\\newline"
+    return sticker
+
+# set output file to .tex
+latex_file_path = output_file_path.with_suffix(".tex")
+
+# remove old output file and ignore error if file does not exist
+try:
+    latex_file_path.unlink()
+except (FileNotFoundError):
+    pass
+
+# Round number of pages needed to fit all stickers up to nearest
+# whole page.
+names_number_new = len(names_list_new)
+latex_pages = (names_number_new // 189) + 1
+
+#######################################################################
+# typeset LaTeX file
+#######################################################################
+
+# save latex document preamble in variable
+latex_preamble = \
+"""\\documentclass[a4paper]{article} % document definition
+% used to adjust page margins to 3.5mm
+\\usepackage[top=1.2cm, bottom=1.2cm, left=0.5cm, right=0.5cm]{geometry}
+% used for table with columns of a defined width
+\\usepackage{tabularx}
+% used to add white space after column rows
+\\usepackage{booktabs}
+% to format date
+\\usepackage{datetime2}
+% for more font sizes
+\\usepackage{moresize}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\\pagestyle{empty} % no page numbers
+\\setlength{\\parindent}{0pt} % set paragraph indent to zero
+
+% define new date style
+\\DTMnewdatestyle{mydate}{%
+    \\renewcommand{\\DTMdisplaydate}[4]{%
+"""\
+f"{latex_date}"\
+"""
+    }%
+    \\renewcommand{\\DTMDisplaydate}{\\DTMdisplaydate}%
+}
+\\DTMsetdatestyle{mydate} % set new datestyle as default
+\\newcommand{\\DATE}{\\today} % create alias for current date command
+
+% defines custom column type for table
+\\newcolumntype{Y}{>{\\centering\\arraybackslash}X}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\\begin{document}
+\\batchmode % disable command line output
+
+% scriptsize/ssmall, bold and sans-serif font throughout the entire document
+\\scriptsize \\bfseries \\sffamily
+% table definition: spans the entire page in (text)width
+% @{} removes white space before first and after last row
+% *{7}{Y} defines seven columns of equal width with text centering
+% sample name and date rows alternate with different amounts of spacing\n\n"""
+
+# create .tex file and write to it
+with open(latex_file_path, "a+") as latex_file:
+    latex_file.write(latex_preamble) # write preamble once
+
+    # variable to track the current position in the list of names
+    n = 0
+
+    # loop through pages of final sticker layout
+    for page_number in range(latex_pages):
+        # start each page with the opening of the table environment
+        latex_file.write(f"% Page {page_number+1}\n"
+            "\\begin{tabularx}{\linewidth}{@{}*{7}{Y}@{}}\n")
+
+        # loop through each line of and write sticker contents to it
+        for line_number in range(27):
+            # add tab character at beginning of line
+            latex_file.write("\t")
+            # 
+            for l in range (7):
+                # if names to be printed still left, do so
+                if (n < (names_number_new-1) and l < 6):
+                    latex_file.write(f"{return_sticker(n)} & ")
+                elif (n == (names_number_new-1) or l == 6):
+                    latex_file.write(f"{return_sticker(n)}")
+                else:
+                    break
+                n += 1
+            # end line after 7 stickers
+            latex_file.write(" \\\\")
+            # if line is the last one of the page
+            if (line_number == 26):
+                latex_file.write(" \\addlinespace[0.05cm]\n")
+            # if next line is not the last line of the page
+            else:
+                latex_file.write(" \\addlinespace[0.470878cm]\n")
+            # if all names were printed, break loop
+            if (n == names_number_new):
+                break
+        # close table environment at the end of the page
+        latex_file.write("\\end{tabularx}\n\n")
+    # reenable command line output and end document
+    latex_file.write("\\scrollmode\n\\end{document}")
+
+# call pdflatex to typeset .tex file # text = FALSE
+subprocess.run(["pdflatex", latex_file_path], stdout=subprocess.DEVNULL)
+# open resulting pdf file 
+subprocess.run(["open", latex_file_path.with_suffix(".pdf")])