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ChopUp converts a non-GCG sequence file containing lines longer than 511 characters and as long as 32,000 characters into a new file containing lines no longer than 50 characters. The new file can be read by Reformat to create a GCG-format sequence file.
This program converts a file with long lines to a file with lines no longer than 50 characters, splitting long lines into two or more lines. When possible, lines are split at a blank space.
Here is a session using ChopUp to convert the file gamma.seq to a file with lines no longer than 50 characters:
% chopup CHOPUP what file ? gamma.seq What should I call the chopped file (* gamma.dat *) ? All of "gamma.seq" chopped up without error! %
Here is part of the output file:
!!NA_SEQUENCE 1.0
Human fetal beta globins G and A gamma
from Shen, Slightom and Smithies, Cell 26;
191-203.
Analyzed by Smithies et al. Cell 26; 345-353.
gamma.seq Length: 11375 June 27, 1994 10:09
Type: N Check: 6474 ..
1 GGATCCTAGA TATTCCTTAG TCTGAGGAGG
AGCAATTAAG ATTCACTTGT
51 TTAGAGGCTG GGAGTGGTGG CTCACGCCTG
TAATCCCAGA ATTTTGGGAG
//////////////////////////////////////////
Replace, CompressText, OneCase, ShiftOver, DeTab, ChopUp, LPrint, and ListFile are the Wisconsin Package file utilities programs.
No line in the input file may be longer than 32,000 characters.
Sequence files prepared with a text editor or brought to your computer from other sources may contain lines longer than 511 characters. These sequence files must be converted by ChopUp before being read by Reformat.
All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
Minimal Syntax: % chopup [-INfile=]gamma.seq -Default Prompted Parameters: None Local Data Files: None Optional Parameters: -LENgth=50 sets the maximum line length in the output file -NOMONitor suppresses the screen monitor
None.
You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
sets the maximum line length in the output file. -LENgth can have any value from 2 to 132.
This program normally monitors its progress on your screen. However, when you use -Default to suppress all program interaction, you also suppress the monitor. You can turn it back on with this parameter. If you are running the program in batch, the monitor will appear in the log file.
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