convert 96 well name to numeric position

96well_alpha2numeric.py

#!/usr/bin/env python

import csv
import string
import datetime
import random
import json
import re
import sys
import os


def well96_to_number(well_name):
    """
    Given a Well-Name of a 96-well plate (e.g. "A12" or "F08")
    returns the well number:
        A01 =>  1
        A1  =>  1
        A12 =>  89
        B01 =>  2
        B1  =>  2
        B12 =>  90
    """
    if len(well_name)<2 or len(well_name)>3:
        raise ValueError("invalid well name '%s' (expecting 2 or 3 charracters)" % ( well_name ) )
    row_text = well_name[:1].upper();
    if row_text < 'A' or row_text > 'H':
        raise ValueError("invalid row '%s' in well name '%s' (expecting letter 'A' to 'H')" % ( row_text, well_name ) )
    row = ord(row_text) - ord("A") + 1 ;

    col_text = well_name[1:]
    try:
        col = int(col_text)
    except ValueError:
        raise ValueError("invalid column '%s' in well name '%s' (expecting a numberic value)" % ( col_text, well_name ) )
    if col < 1 or col > 12:
        raise ValueError("invalid column '%s' in well name '%s' (expecting a number between 1 and 12)" % ( col_text, well_name ) )

    well_num = (col-1)*8 + row
    return well_num

def convert_number():
    if len(sys.argv)<2:
        sys.stderr.write("Usage: %s [WELL-NAME]\n" % ( sys.argv[0] ))
        sys.exit(1)
    well_num = well96_to_number(sys.argv[1])
    print well_num

def csv96_wellname_to_number(filename):
    """
    Given a filename of a CSV containing well-names in the second and fourth columns,
    convert the well-names (e.g. "A11") to well-number (e.g. "81").

    The CSV is expected to have 6 fields:
        source plate,
        source well name (e.g. "A11")
        dest plate,
        dest well name (e.g. "B09")
        [other optional columns]
    """
    line_number = 0
    try:
        for line_number,row in enumerate(csv.reader(open(filename))):
            if line_number==0: # skip header line
                print ",".join(row)
                continue

            if len(row) < 4:
                raise Exception("expecting at least 4 fields")

            row = [ x.strip() for x in row ]

            row[1] = str( well96_to_number( row[1] ) )
            row[3] = str ( well96_to_number( row[3] ) )

            print ",".join(row)
    except IOError as e:
        raise Exception("Error loading CSV file (%s): %s" % ( filename , str(e)))
    except ValueError as e:
        raise Exception("Invalid input in CSV file '%s' line %d: %s" % ( filename, line_number+1, str(e) ) )


def convert_csvfile():
    if len(sys.argv)<2:
        sys.stderr.write("Usage: %s [CSV-FILE]\n" % ( sys.argv[0] ))
        sys.exit(1)
    csv96_wellname_to_number(sys.argv[1])

if __name__ == "__main__":
    convert_csvfile()