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awk getline problem

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# 1  
Old 12-13-2012
awk getline problem
Hello,
I want to print out the DNA sequence entries (tens of thousand!) that are longer than certain value (i=200) from a file (FASTA file) as:
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 tried:
Code:
awk '! /^>S/ { next } { getline seq } (length(seq) >= i) { print $0 "\n" seq }' i=200 infile.fasta

Nothing was print out.
I noticed the DNA sequence line are 60bp wide, if my i is less than 60, only the header (the lines with ">" as separator) and the first sequence line were printed, but I am expecting all sequence lines under each header. If the i is bigger than 60, nothing was printed. For sure most of the entries in the infile.fasta are longer than 60bp. Did I miss anything?
Thanks a lot!
# 2  
Old 12-13-2012
getline gets lines, it doesn't paste them together.

I don't think you need getline here in any case, awk doesn't need getline's help to read lines one at a time from the default source.

It'd be helpful to see what this program should be doing, not just what it isn't.
This User Gave Thanks to Corona688 For This Post:
yifangt
# 3  
Old 12-13-2012
I *think* this is what you want.
awk -v len=200 -f yi.awk myFile
yi.awk:
Code:
function doPrint(r,h,   n)
{
     n=gsub(RS,RS,r)
     if (length(r)-n>len)
       print h RS r
}
/^>S/ {
   if (h) {
     doPrint(r,h)
     r=""
   }
   h=$0
   next
}
{r=(r)?r RS $0:$0}
END {
  doPrint(r,h)
}

This User Gave Thanks to vgersh99 For This Post:
yifangt
# 4  
Old 12-13-2012
The interesting part is the script works with another fasta file in which each sequence line/row has more 120bp wide.
Code:
>S94D_ctg_8004 Average coverage: 402.95
ATAATGCCTGTGAATATGACATGTGTTCCTGTTTCTACATCAGACTACTATTCTTGCATATCCCGCATCAGTCACTTATGATAAGGCACCTTTAAGTCGCCACTGTGATATTGGTTGTGT
CTTGCATATGATTTCTAGCATGTACTGCTTCTAATTTGTTGAAACGCCATACAGTTTGAACTTGGCAGAGTGATATTGGTTGCATCTTTCATATGGTGTCTAGCTTGCAGTGCTTCTAAT
TT
>S94D_ctg_8022 Average coverage: 212.74
CGTTGTCTGTGTGACATTTAAGAGTGTTTTGTGCAGTGCAACAAAAGGTCACAATGGCAACGAGGTGAAGTAGATAACCCTGTTTACACAGAGGTGCAAAGGAAACAACTAGTGGTCAAT
AACCCTGTTTACCAGCACCATGTGCATCTACCGATGTACTGGGGTGATGCACAGTCTGTTG
>S94D_ctg_8062 Average coverage: 710.87
ATGAATTTCAGACGAGTTTTGGATTTACTAGAATTTAAAAACCAGGCATCTCAATGTTTTGCCGGCAATCAACGGTGCCCTGGTGTTTGAAATTCATTCCCATTTCTTGCATGGGACCTA
AGCATGCACCCAAGGACA
>S94D_ctg_9034 Average coverage: 37.84
AGATTATTTTGTCTGCCATGTATAATTTTGGTTGATGTTTAGCCTGTTGTGCTTAACATGCTTCTCGACGTACCTACACAGGACAATTTGGGAACGACTGCTGTTTTCCATCGAGGTTAG
TTTCATCCCATGGCTTATATCTGCTCAATGTTCAGGATATCGGTAGCCGGTACCATATAGGCCGGCGGCTGATAGGAGACTAATCGGTGAATCGGACT

I thought the script may be related to the newline, but I did check and could not find any abnormal. Not sure the EOL is really the same of the two files. I will check it. Thank you both!
# 5  
Old 12-13-2012
A program which doesn't do what you want really doesn't help explain what you do want, and you still haven't showed output demonstrating what you actually want. So we're still a bit in the dark, here.
# 6  
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!
# 7  
Old 12-13-2012
Do you have GNU awk? You can change the meaning of 'record' with RS, split on > instead of \n, and count the length more directly:

Code:
awk -v RS="\n>" -F"\n" '{ V=$0; gsub(/\n/, "", V); if((length(V)-length($1)) > 200) print ">"$0 }'
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