Make a plate record

This program makes a plate record (sample sheet) for the HMS Biopolymers Facility ABI 3700 (genotyping runs), starting from a 12 x 8 array of sample names that you have created in Excel and saved as tab-delimited text. The letters A-H at the left, denoting rows, are essential in the input file. Other lines will be ignored.

Give a VERY short, descriptive name for this plate. I recommend using your initials and an index number, e.g., "SRD001". Note that this will end up as part of every sample file name. Spaces will be deleted.

Select the tab-delimited text file to upload:

Transpose panel name/number from end to beginning? (That is, AAA_pBB will be changed to pBB_AAA, where AAA and BB stand for any text. The underscore before "p" or "P" is required.)

The output is also tab-delimited text. Make sure you save the result in text format with a filename of, let's say, CN-C.plt.txt. Note: I have found that a recent version of Netscape doesn't save the file properly (all lanes become "blank"), and Internet Explorer inserts two unwanted blank lines at the top. Use Safari instead.

Here's an example of a spreadsheet to upload. Notice that sample names include the family code (CN), individual code (2 through 552), and panel number (13 through 19). Keep them short. Spaces will be removed.

In order for various other of my scripts to work correctly, sample names must follow a particular naming convention:

panel-name underscore family-code dash individual-code
where

Since sample names become part of the file names, no spaces or punctuation other than underscore, dash, and dot are allowed.

    123456789101112
Ap13_CN-2p14_CN-2p15_CN-2p16_CN-2p17_CN-2p18_CN-2p19_CN-2p13_CN-3p13_CN-31p13_CN-33p13_CN-41p13_CN-42
Bp13_CN-51p14_CN-51p15_CN-51p16_CN-51p17_CN-51p18_CN-51p19_CN-51p14_CN-3p14_CN-31p14_CN-33p14_CN-41p14_CN-42
Cp13_CN-55p14_CN-55p15_CN-55p16_CN-55p17_CN-55p18_CN-55p19_CN-55p15_CN-3p15_CN-31p15_CN-33p15_CN-41p15_CN-42
Dp13_CN-512p14_CN-512p15_CN-512p16_CN-512p17_CN-512p18_CN-512p19_CN-512p16_CN-3p16_CN-31p16_CN-33p16_CN-41p16_CN-42
Ep13_CN-513p14_CN-513p15_CN-513p16_CN-513p17_CN-513p18_CN-513p19_CN-513p17_CN-3p17_CN-31p17_CN-33p17_CN-41p17_CN-42
Fp13_CN-552p14_CN-552p15_CN-552p16_CN-552p17_CN-552p18_CN-552p19_CN-552p18_CN-3p18_CN-31p18_CN-33p18_CN-41p18_CN-42
Gp13_CN-330p14_CN-330p15_CN-330p16_CN-330p17_CN-330p18_CN-330p19_CN-330p19_CN-3p19_CN-31p19_CN-33p19_CN-41p19_CN-42
Hp13_CN-332p14_CN-332p15_CN-332p16_CN-332p17_CN-332p18_CN-332p19_CN-332p13_CN-5p14_CN-5p15_CN-5p16_CN-5p17_CN-5

Try it yourself:

Steve DePalma, depalma & rascal.med.harvard
http://genetics.med.harvard.edu/~depalma
July 8, 2004