Help with reformat single-line multi-fasta into multi-line multi-fasta


 
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# 1  
Old 06-13-2018
Help with reformat single-line multi-fasta into multi-line multi-fasta

Input File:
Code:
>Seq1
ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD
>Seq2
SDASDAQEQWEQeqAdfaasd
>Seq3
ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG
......

Desired Output File
Code:
>Seq1
ASDADAFASF
ASFADGSDGF
SDFSDFSDFS
DFSDFSDFSD
FSDFSDFSDF
SD
>Seq2
SDASDAQEQW
EQeqAdfaasd
>Seq3
ASDSALGHIU
DFJANCAGPA
THLACJHPAU
TYNJKG
......

Any idea how to reformat a single-line multi-fasta into 10 words/symbols per line multi-fasta file?

Thanks for any advice.
# 2  
Old 06-13-2018
Did you consider
Code:
fold -b10 file
>Seq1
ASDADAFASF
ASFADGSDGF
SDFSDFSDFS
DFSDFSDFSD
FSDFSDFSDF
SD
>Seq2
SDASDAQEQW
EQeqAdfaas
d
>Seq3
ASDSALGHIU
DFJANCAGPA
THLACJHPAU
TYNJKG

# 3  
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.
# 4  
Old 06-14-2018
Try (GNU sed):
Code:
sed '/^>/!s/.\{10\}/&\n/g' infile

Regular sed:
Code:
sed '/^>/!s/.\{10\}/&\
/g' infile

# 5  
Old 06-15-2018
Also
Code:
fold -b -w 50 input_file

works on many *x systems, and should not have a problem with large files.
If there is a 2GB limit (happens if compiled with 32-bit and without largefile support), then it can help to let the shell open it (assuming the shell is either 64-bit or with largefile support).
Code:
fold -b -w 50 < input_file

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