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# 1  
Old 08-21-2014
Delete some words
hi, i have a fasta file like this:
Code:
>contig00003  length=363  numreads=45  gene=isogroup00001  status=it_thresh
GATTTTTTACCCTGGGAGTGAGGAGGACGAGGTTGAGGATGAAGAAAAGAGAAAGATGAAGAGGTTGAGGATGTT
GTAGTCGGCGGTGGAATTAGGGGGAGCCGGCGAGCCCAAGTATTTTGCAGAGGTGTCTTCATCATCCAAACAACA
CGAGAGGGTGCAATTTGGTCTCTGCGTTGTTATAGATCCAAAGTTTTTGGACCCTGTTTGGCATCGTGTATCAAGTA
TTGGTTACACAGTCTATATTTTCAAGAACGAGACTGTGAAAGCTGTAAGCAACTTTTTATTtATCTATTTATTTTTATG
CTATAGCTTAtattaaactta
>contig00010  length=760  numreads=49  gene=isogroup00001  status=it_thresh
TCAAAGTTTTAGGTTCCAATTTGTATGGCTCAACTTAAGAAGTTTGTTGTAAAAAaGGAAATTCTTTCTGATCTATTA
GGGGCAGAAGTGCCACAATATATGAAGTTGAGAAATTAAaTAAAGTAATCATAGTACATTGTCTCGTTTGGATAGAC
GTAGGCTCTCAaGAAAAAAaGTTCTCATAGTTCTTGATGATGTGGATGATTTAGTGCGGCAAGTAGAACCTGGTCAA
GGGAGTAGAATAATTATGACAAGCAGAGATAGACAATTGAGTGAAGCTCTCTGCCTGTTTTGCAAGCATGCCTTCAA
GCGACAATTTCTAAGAACAGGATATTTAATAAGGCAATTGATCATGCTCAGGG
>G383C4U02H6B5W length=257
CCGGGCTCCCCATCTTCTCTATCTCTTGTGTGATTGTTGCAGAATACATCAAAGACTTGGGGTTGAGAGAGACAGCA
TCATAAACCTGATCACGGAAGCCCCTTTGAAGCATGCAGTCCACCTCATCTAGCCTTGTTGTCGTTGAAATAGTCCAT
CTGCCATCTTTAAATACATGCGCAACATAATGCCCGCATTGCGTATCTAGTCCAATATCATGCTTTATTAAAAAGATCA
ATAAGCCTTCCTGGAGTCCCCACAATCAAGTTCCAACTCCTTGCTGAAATGCGGTAGAGTTGTCCAGCCATCA
>G383C4U02IH1AO length=105
TTCAAGGAACTTTCATCCATCCAATGATCTAACCAATTTGAACCTAGTTTTGATTCATCTCTGAAGTTCGAATTTGAAC
CACATTCTTAAGAATTGAGGGCCCATCAAATTTAGTACTATAATCATGAAGTAGGTGATCCTCTCTTGTCACTCTTTTC
ATCATCAGCAAGATGACTTCTCATTGGAATGCTACCATGCTTGTTCCAAAA

.....

How can i remove the additional information for each sequence and get a file like this:
Code:
>contig00003
GATTTTTTACCCTGGGAGTGAGGAGGACGAGGTTGAGGATGAAGAAAAGAGAAAGATGAAGAGGTTGAGGATGTT
GTAGTCGGCGGTGGAATTAGGGGGAGCCGGCGAGCCCAAGTATTTTGCAGAGGTGTCTTCATCATCCAAACAACA
CGAGAGGGTGCAATTTGGTCTCTGCGTTGTTATAGATCCAAAGTTTTTGGACCCTGTTTGGCATCGTGTATCAAGTA
TTGGTTACACAGTCTATATTTTCAAGAACGAGACTGTGAAAGCTGTAAGCAACTTTTTATTtATCTATTTATTTTTATG
CTATAGCTTAtattaaactta
>contig00010
TCAAAGTTTTAGGTTCCAATTTGTATGGCTCAACTTAAGAAGTTTGTTGTAAAAAaGGAAATTCTTTCTGATCTATTA
GGGGCAGAAGTGCCACAATATATGAAGTTGAGAAATTAAaTAAAGTAATCATAGTACATTGTCTCGTTTGGATAGAC
GTAGGCTCTCAaGAAAAAAaGTTCTCATAGTTCTTGATGATGTGGATGATTTAGTGCGGCAAGTAGAACCTGGTCAA
GGGAGTAGAATAATTATGACAAGCAGAGATAGACAATTGAGTGAAGCTCTCTGCCTGTTTTGCAAGCATGCCTTCAA
GCGACAATTTCTAAGAACAGGATATTTAATAAGGCAATTGATCATGCTCAGGG
>G383C4U02H6B5W
CCGGGCTCCCCATCTTCTCTATCTCTTGTGTGATTGTTGCAGAATACATCAAAGACTTGGGGTTGAGAGAGACAGCA
TCATAAACCTGATCACGGAAGCCCCTTTGAAGCATGCAGTCCACCTCATCTAGCCTTGTTGTCGTTGAAATAGTCCAT
CTGCCATCTTTAAATACATGCGCAACATAATGCCCGCATTGCGTATCTAGTCCAATATCATGCTTTATTAAAAAGATCA
ATAAGCCTTCCTGGAGTCCCCACAATCAAGTTCCAACTCCTTGCTGAAATGCGGTAGAGTTGTCCAGCCATCA
>G383C4U02IH1AO
TTCAAGGAACTTTCATCCATCCAATGATCTAACCAATTTGAACCTAGTTTTGATTCATCTCTGAAGTTCGAATTTGAAC
CACATTCTTAAGAATTGAGGGCCCATCAAATTTAGTACTATAATCATGAAGTAGGTGATCCTCTCTTGTCACTCTTTTC
ATCATCAGCAAGATGACTTCTCATTGGAATGCTACCATGCTTGTTCCAAAA

.....


Thanks
# 2  
Old 08-21-2014
Code:
awk '/^>/ { NF=1 } 1' inputfile > outputfile

This User Gave Thanks to Corona688 For This Post:
the_simpsons
# 3  
Old 08-21-2014
Thanks, that works perfectly.
Quote:
Originally Posted by Corona688
Code:
awk '/^>/ { NF=1 } 1' inputfile > outputfile

This User Gave Thanks to the_simpsons For This Post:
Corona688
# 4  
Old 08-21-2014
Hello the_simpsons,

The following may also help.

Code:
awk '/^>/ {$0=$1} 1'  filename

Output will be as follows.


Code:
>contig00003
GATTTTTTACCCTGGGAGTGAGGAGGACGAGGTTGAGGATGAAGAAAAGAGAAAGATGAAGAGGTTGAGGATGTT
GTAGTCGGCGGTGGAATTAGGGGGAGCCGGCGAGCCCAAGTATTTTGCAGAGGTGTCTTCATCATCCAAACAACA
CGAGAGGGTGCAATTTGGTCTCTGCGTTGTTATAGATCCAAAGTTTTTGGACCCTGTTTGGCATCGTGTATCAAGTA
TTGGTTACACAGTCTATATTTTCAAGAACGAGACTGTGAAAGCTGTAAGCAACTTTTTATTtATCTATTTATTTTTATG
CTATAGCTTAtattaaactta
>contig00010
TCAAAGTTTTAGGTTCCAATTTGTATGGCTCAACTTAAGAAGTTTGTTGTAAAAAaGGAAATTCTTTCTGATCTATTA
GGGGCAGAAGTGCCACAATATATGAAGTTGAGAAATTAAaTAAAGTAATCATAGTACATTGTCTCGTTTGGATAGAC
GTAGGCTCTCAaGAAAAAAaGTTCTCATAGTTCTTGATGATGTGGATGATTTAGTGCGGCAAGTAGAACCTGGTCAA
GGGAGTAGAATAATTATGACAAGCAGAGATAGACAATTGAGTGAAGCTCTCTGCCTGTTTTGCAAGCATGCCTTCAA
GCGACAATTTCTAAGAACAGGATATTTAATAAGGCAATTGATCATGCTCAGGG
>G383C4U02H6B5W
CCGGGCTCCCCATCTTCTCTATCTCTTGTGTGATTGTTGCAGAATACATCAAAGACTTGGGGTTGAGAGAGACAGCA
TCATAAACCTGATCACGGAAGCCCCTTTGAAGCATGCAGTCCACCTCATCTAGCCTTGTTGTCGTTGAAATAGTCCAT
CTGCCATCTTTAAATACATGCGCAACATAATGCCCGCATTGCGTATCTAGTCCAATATCATGCTTTATTAAAAAGATCA
ATAAGCCTTCCTGGAGTCCCCACAATCAAGTTCCAACTCCTTGCTGAAATGCGGTAGAGTTGTCCAGCCATCA
>G383C4U02IH1AO
TTCAAGGAACTTTCATCCATCCAATGATCTAACCAATTTGAACCTAGTTTTGATTCATCTCTGAAGTTCGAATTTGAAC
CACATTCTTAAGAATTGAGGGCCCATCAAATTTAGTACTATAATCATGAAGTAGGTGATCCTCTCTTGTCACTCTTTTC
ATCATCAGCAAGATGACTTCTCATTGGAATGCTACCATGCTTGTTCCAAAA


EDIT: Adding one more solution for same.

Code:
[singh@localhost awk_programming]$ awk '/^>/ {print $1} !/^>/ {print $0}' filename

Code:
>contig00003
GATTTTTTACCCTGGGAGTGAGGAGGACGAGGTTGAGGATGAAGAAAAGAGAAAGATGAAGAGGTTGAGGATGTT
GTAGTCGGCGGTGGAATTAGGGGGAGCCGGCGAGCCCAAGTATTTTGCAGAGGTGTCTTCATCATCCAAACAACA
CGAGAGGGTGCAATTTGGTCTCTGCGTTGTTATAGATCCAAAGTTTTTGGACCCTGTTTGGCATCGTGTATCAAGTA
TTGGTTACACAGTCTATATTTTCAAGAACGAGACTGTGAAAGCTGTAAGCAACTTTTTATTtATCTATTTATTTTTATG
CTATAGCTTAtattaaactta
>contig00010
TCAAAGTTTTAGGTTCCAATTTGTATGGCTCAACTTAAGAAGTTTGTTGTAAAAAaGGAAATTCTTTCTGATCTATTA
GGGGCAGAAGTGCCACAATATATGAAGTTGAGAAATTAAaTAAAGTAATCATAGTACATTGTCTCGTTTGGATAGAC
GTAGGCTCTCAaGAAAAAAaGTTCTCATAGTTCTTGATGATGTGGATGATTTAGTGCGGCAAGTAGAACCTGGTCAA
GGGAGTAGAATAATTATGACAAGCAGAGATAGACAATTGAGTGAAGCTCTCTGCCTGTTTTGCAAGCATGCCTTCAA
GCGACAATTTCTAAGAACAGGATATTTAATAAGGCAATTGATCATGCTCAGGG
>G383C4U02H6B5W
CCGGGCTCCCCATCTTCTCTATCTCTTGTGTGATTGTTGCAGAATACATCAAAGACTTGGGGTTGAGAGAGACAGCA
TCATAAACCTGATCACGGAAGCCCCTTTGAAGCATGCAGTCCACCTCATCTAGCCTTGTTGTCGTTGAAATAGTCCAT
CTGCCATCTTTAAATACATGCGCAACATAATGCCCGCATTGCGTATCTAGTCCAATATCATGCTTTATTAAAAAGATCA
ATAAGCCTTCCTGGAGTCCCCACAATCAAGTTCCAACTCCTTGCTGAAATGCGGTAGAGTTGTCCAGCCATCA
>G383C4U02IH1AO
TTCAAGGAACTTTCATCCATCCAATGATCTAACCAATTTGAACCTAGTTTTGATTCATCTCTGAAGTTCGAATTTGAAC
CACATTCTTAAGAATTGAGGGCCCATCAAATTTAGTACTATAATCATGAAGTAGGTGATCCTCTCTTGTCACTCTTTTC
ATCATCAGCAAGATGACTTCTCATTGGAATGCTACCATGCTTGTTCCAAAA

Thanks,
R. Singh
Last edited by RavinderSingh13; 08-21-2014 at 01:31 PM..
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