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Top Forums Shell Programming and Scripting Split file into multiple files Post 302447611 by jdhahbi on Monday 23rd of August 2010 08:21:49 PM
Old 08-23-2010
Split file into multiple files

Hi

I have a file that has multiple sequences; the sequence name is the line starting with '>'. It looks like below:
infile.txt:
Code:
>HE_ER
tttggtgccttgactcggattgggggacctcccttgggagatcaatcccctgtcctcctgctctttgctc
cgtgaaaaggatccacctatgacctctagtcctcagacccaccagcccaaggaacatctcaccaatttca
>M7B_Ho_sap
tgagaactgcagaactctcggcacagaacaactccatccaaacccctgcactaagagacttgaccaaact
aactagtgtccggctttgtttatctttgaca
>LT_H_ss
gtgagacaaagtaacaaatgtaagaagccatgtctgctcatttctgcttgccaacataatttcacaaagc
ccctgactctgtgatgacatgcagctctcnagaaagatgctttgaagacaaarcaggatrgagcacacag
ccccccayrtctcttgcctgagtcactayattccttaaaagataaatgaccctagtccttgccttttcct
>L_5_Et
ttaaaaacaaagcgggagacttccgcttccgggaagatggagtagacgtacttttccctattcctcccgc
taagtacaactaaaaaccctggacattatatataaaacaaacataagaagactctgaaaggtggagagaa

I need to extract the sequnces in individual files; the sequence name will be the file name. The output files will be like:

HE_ER.fa:
Code:
>HE_ER
tttggtgccttgactcggattgggggacctcccttgggagatcaatcccctgtcctcctgctctttgctc
cgtgaaaaggatccacctatgacctctagtcctcagacccaccagcccaaggaacatctcaccaatttca

M7B_Ho_sap.fa:
Code:
>M7B_Ho_sap
tgagaactgcagaactctcggcacagaacaactccatccaaacccctgcactaagagacttgaccaaact
aactagtgtccggctttgtttatctttgaca

LT_H_ss.fa:

Code:
>LT_H_ss
gtgagacaaagtaacaaatgtaagaagccatgtctgctcatttctgcttgccaacataatttcacaaagc
ccctgactctgtgatgacatgcagctctcnagaaagatgctttgaagacaaarcaggatrgagcacacag
ccccccayrtctcttgcctgagtcactayattccttaaaagataaatgaccctagtccttgccttttcct

L_5_Et.fa:
Code:
>L_5_Et
ttaaaaacaaagcgggagacttccgcttccgggaagatggagtagacgtacttttccctattcctcccgc
taagtacaactaaaaaccctggacattatatataaaacaaacataagaagactctgaaaggtggagagaa

I searched for some examples and so far I tried:

Code:
awk -v a=">" '{print $0 >> ($1a".fa")}' infile.txt

but it is not working for me. Please help

Joseph
 

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unix2dos(1)						      General Commands Manual						       unix2dos(1)

NAME
unix2dos - UNIX to DOS text file format converter SYNOPSYS
unix2dos [options] [-c convmode] [-o file ...] [-n infile outfile ...] Options: [-hkqV] [--help] [--keepdate] [--quiet] [--version] DESCRIPTION
This manual page documents unix2dos, the program that converts text files in UNIX format to DOS format. OPTIONS
The following options are available: -h --help Print online help. -k --keepdate Keep the date stamp of output file same as input file. -q --quiet Quiet mode. Suppress all warning and messages. -V --version Prints version information. -c --convmode convmode Sets conversion mode. Simulates unix2dos under SunOS. -o --oldfile file ... Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used. -n --newfile infile outfile ... New file mode. Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be used or you WILL lost your files. EXAMPLES
Get input from stdin and write output to stdout. unix2dos Convert and replace a.txt. Convert and replace b.txt. unix2dos a.txt b.txt unix2dos -o a.txt b.txt Convert and replace a.txt in ASCII conversion mode. Convert and replace b.txt in ISO conversion mode. unix2dos a.txt -c iso b.txt unix2dos -c ascii a.txt -c iso b.txt Convert and replace a.txt while keeping original date stamp. unix2dos -k a.txt unix2dos -k -o a.txt Convert a.txt and write to e.txt. unix2dos -n a.txt e.txt Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt. unix2dos -k -n a.txt e.txt Convert and replace a.txt. Convert b.txt and write to e.txt. unix2dos a.txt -n b.txt e.txt unix2dos -o a.txt -n b.txt e.txt Convert c.txt and write to e.txt. Convert and replace a.txt. Convert and replace b.txt. Convert d.txt and write to f.txt. unix2dos -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt DIAGNOSTICS
BUGS
The program does not work properly under MSDOS in stdio processing mode. If you know why is that so, please tell me. AUTHOR
Benjamin Lin - ( blin@socs.uts.edu.au ) MISCELLANY
Tested environment: Linux 1.2.0 with GNU C 2.5.8 SunOS 4.1.3 with GNU C 2.6.3 MS-DOS 6.20 with Borland C++ 4.02 Suggestions and bug reports are welcome. SEE ALSO
dos2unix(1) 1995.03.31 unix2dos v2.2 unix2dos(1)
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