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Top Forums Shell Programming and Scripting Help with reformat single-line multi-fasta into multi-line multi-fasta Post 303018743 by patrick87 on Thursday 14th of June 2018 04:45:44 AM
Old 06-14-2018
Hi RudiC,

It seems like no work when my data is huge?
eg.
Input file
Code:
cat input_file
>scaffold1|size134247
TCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Output file
Code:
fold -b50 input_file
>scaffold1|size134247
TCTCTGTCTCTCTCTCTCTCTCTCTCTC
TCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Desired Output file
Code:
>scaffold1|size134247
TCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTG
TGTGTGTGTGTGTGTGTGTGTGTGTGTG

I believe fold command will take header into account too?
I wanna split a single-line multi-fasta (exclude >header) into 10 words/symbols per line multi-fasta file.

Thanks for any advice.
 

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fold(1) 						      General Commands Manual							   fold(1)

NAME
fold - fold long lines for finite width output device SYNOPSIS
width] [file ...] Obsolete form: width] [file ...] DESCRIPTION
The command is a filter that folds the contents of the specified files, breaking the lines to have a maximum of width column positions (or bytes, if the option is specified). The command breaks lines by inserting a newline character so that each output line is the maximum width possible that does not exceed the specified number of column positions (or bytes). A line cannot be broken in the middle of a char- acter. If no files are specified or if a file name of is specified, the standard input is used. The command is often used to send text files to line printers that truncate, rather than fold, lines wider than the printer is able to print. If the backspace, tab, or carriage-return characters are encountered in the input, and the option is not specified, they are treated spe- cially as follows: Backspace The current count of line width is decremented by one, although the count never becomes negative. Thus, the char- acter sequence character-backspace-character counts as using one column position, assuming both characters each occupy a single column position. does not insert a newline character immediately before or after any backspace character. Tab Each tab character encountered advances the column position pointer to the next tab stop. Tab stops are set 8 col- umns apart at column positions 1, 9, 17, 25, 33, etc. Carriage-return The current count of line width is set to zero. does not insert a newline character immediately before or after any carriage-return character. Note that may affect any underlining that is present. Options The command recognizes the following options and command-line arguments: Count width in bytes rather than in column positions. Break the line on the last blank character found before the specified number of column positions (or bytes). If none are found, break the line at the specified line length. Specify the maximum line length, in column positions (or bytes if is specified). The default value is 80. width should be a multiple of 8 if tabs are present, or the tabs should be expanded using before processing by (see expand(1)). The option is obsolescent and may be removed in a future release. EXTERNAL INFLUENCES
Environment Variables determines the interpretation of text as single- and/or multi-byte characters. determines the language in which messages are displayed. If or is not specified in the environment or is set to the empty string, the value of is used as a default for each unspecified or empty variable. If is not specified or is set to the empty string, a default of "C" (see lang(5)) is used instead of If any internationalization variable contains an invalid setting, behaves as if all internationalization variables are set to "C". See environ(5). International Code Set Support Single- and multi-byte character code sets are supported. SEE ALSO
expand(1). STANDARDS CONFORMANCE
fold(1)
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