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Full Discussion: awk getline problem
Top Forums Shell Programming and Scripting awk getline problem Post 302743911 by yifangt on Thursday 13th of December 2012 02:34:10 PM
Old 12-13-2012
Hi, Corona:
For example, infile:
Code:
>S94D_ctg_8004 Average coverage: 402.95
ATAATGCCTGTGAATATGACATGTGTTCCTGTTTCTACATCAGACTACTATTCTTGCATA
TCCCGCATCAGTCACTTATGATAAGGCACCTTTAAGTCGCCACTGTGATATTGGTTGTGT
CTTGCATATGATTTCTAGCATGTACTGCTTCTAATTTGTTGAAACGCCATACAGTTTGAA
CTTGGCAGAGTGATATTGGTTGCATCTTTCATATGGTGTCTAGCTTGCAGTGCTTCTAAT
TT
>S94D_ctg_8022 Average coverage: 212.74
CGTTGTCTGTGTGACATTTAAGAGTGTTTTGTGCAGTGCAACAAAAGGTCACAATGGCAA
CGAGGTGAAGTAGATAACCCTGTTTACACAGAGGTGCAAAGGAAACAACTAGTGGTCAAT
AACCCTGTTTACCAGCACCATGTGCATCTACCGATGTACTGGGGTGATGCACAGTCTGTT
G
>S94D_ctg_8062 Average coverage: 710.87
ATGAATTTCAGACGAGTTTTGGATTTACTAGAATTTAAAAACCAGGCATCTCAATGTTTT
GCCGGCAATCAACGGTGCCCTGGTGTTTGAAATTCATTCCCATTTCTTGCATGGGACCTA
AGCATGCACCCAAGGACA
>S94D_ctg_9034 Average coverage: 37.84
AGATTATTTTGTCTGCCATGTATAATTTTGGTTGATGTTTAGCCTGTTGTGCTTAACATG
CTTCTCGACGTACCTACACAGGACAATTTGGGAACGACTGCTGTTTTCCATCGAGGTTAG
TTTCATCCCATGGCTTATATCTGCTCAATGTTCAGGATATCGGTAGCCGGTACCATATAG
GCCGGCGGCTGATAGGAGACTAATCGGTGAATCGGACT

I want all the entries with sequence less than 200bp are filtered to get outfile as:
Code:
>S94D_ctg_8004 Average coverage: 402.95
ATAATGCCTGTGAATATGACATGTGTTCCTGTTTCTACATCAGACTACTATTCTTGCATA
TCCCGCATCAGTCACTTATGATAAGGCACCTTTAAGTCGCCACTGTGATATTGGTTGTGT
CTTGCATATGATTTCTAGCATGTACTGCTTCTAATTTGTTGAAACGCCATACAGTTTGAA
CTTGGCAGAGTGATATTGGTTGCATCTTTCATATGGTGTCTAGCTTGCAGTGCTTCTAAT
TT
>S94D_ctg_9034 Average coverage: 37.84
AGATTATTTTGTCTGCCATGTATAATTTTGGTTGATGTTTAGCCTGTTGTGCTTAACATG
CTTCTCGACGTACCTACACAGGACAATTTGGGAACGACTGCTGTTTTCCATCGAGGTTAG
TTTCATCCCATGGCTTATATCTGCTCAATGTTCAGGATATCGGTAGCCGGTACCATATAG
GCCGGCGGCTGATAGGAGACTAATCGGTGAATCGGACT

There are some bioperl script for this job, but I like awk that can do it in a flash. Thanks!
 

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IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME
igawk - gawk with include files SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ... igawk [ all gawk options ] [ -- ] program-text file ... DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1). AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like @include getopt.awk in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path. OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports. EXAMPLES
cat << EOF > test.awk @include getopt.awk BEGIN { while (getopt(ARGC, ARGV, "am:q") != -1) ... } EOF igawk -f test.awk SEE ALSO
gawk(1) Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995. AUTHOR
Arnold Robbins (arnold@skeeve.com). Free Software Foundation Nov 3 1999 IGAWK(1)
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