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Help: Parsing a file to new output files

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# 1  
Old 01-10-2013
Help: Parsing a file to new output files
I have an output file similar to this

Code:
>HWI-ST766:129:D0WJDACXX:4:2308:16645:199681.1 /start=1 /end=100 /strand=+ Eukaryotic18S_rRNA
GATTAAGCCATGCATGTGTAAGTTTAAAGTCCTAGAAGGATGAAACTGCGGACGGCTCAT
TATAACAGTAATAGTTTCTTTGGTTAGTATCTATAAGGAT
>HWI-ST766:129:D0WJDACXX:4:2308:2922:199946.1 /start=1 /end=96 /strand=+ Eukaryotic:28S_rRNA
CCTAACTATACGCTCATCAGATACCACAAAAGGTGTTGATTCATCTAAACAGCAGGGCGG
TGGACATAGAAGTCGTTACCCGCTAAGGAGTGTGTC
>HWI-ST766:129:D0WJDACXX:4:2308:5144:199799.1 /start=1 /end=85 /strand=- Bacterial:16S_rRNA
GGGGAGATCTCAAAGAGTCAGGTTGCTTGGAACTGCAGCCTTAAGCGGGAGATATGAAAC
TTCCAAAGCTAAATATAGATGGGAG
>HWI-ST766:129:D0WJDACXX:4:2308:7062:199913.1 /start=2 /end=100 /strand=+ Bacterial:23S_rRNA
TTCGAGTTGGAGCACGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGCG
AAGCCAGAGGAAACTCTGGTGGAGGCTCGAAGCGATACT
>HWI-ST766:129:D0WJDACXX:4:2308:13310:199841.1 /start=10 /end=99 /strand=+ Archaeal:16S_rRNA
AACACAAACTAGCTTGGAGACATCAGCACGTGCCCTTGGAAGAGTTTTCTTTTCTTCTTA
ACATGTATGAGGCCTTGAAATTGGATTACC
>HWI-ST766:129:D0WJDACXX:4:2308:15549:199820.1 /start=1 /end=100 /strand=- Archaeal:23S_rRNA
CCTCAGGATAGCAGGAACAATATTGCAGTTTTATCAGGTAAAGCGAATGATTAGAGGTTA
CTGAGCGTTTTTTGTTTGGACCTATTCTCAAACTTTAAAT
>HWI-ST766:129:D0WJDACXX:4:2308:1510:200068.1 /start=1 /end=100 /strand=- Bacterial:23S_rRNA
GAAGCGGTGTTGACGTGCAAATCACTCGTCAAATTTGGGTATAGGGGCGAAAGACTAATC
GAACCATCTAGTAGCTGGTTCCCTCTGAAGTTTCCCTCAG
>HWI-ST766:129:D0WJDACXX:4:2308:2254:200148.1 /start=1 /end=100 /strand=- Archaeal:23S_rRNA
GATGGTGAACTATACTTGAACGGTTAGAAGCCGAAGGAAACTTTGGTGGAAGAACCACGC
AGTGTTAACGTGCAAATTACTTGTCATATTTGAGTATAGG
>HWI-ST766:129:D0WJDACXX:4:2308:4747:200053.1 /start=2 /end=96 /strand=+ Eukaryotic:28S_rRNA
AGATGACTCGCTGGACTTAAGCATATTATTAAGCGAAGGAAAAGAAATTAACAAAGATTG
CCTTAGTAAGGGCGACTGAACCGGCAATAGCTCGA
>HWI-ST766:129:D0WJDACXX:4:2308:4747:200053.1 /start=2 /end=96 /strand=+ Bacterial:16S_rRNA
AGATGACTCGCTGGACTTAAGCATATTATTAAGCGAAGGAAAAGAAATTAACAAAGATTG
CCTTAGTAAGGGCGACTGAACCGGCAATAGCTCGA
>HWI-ST766:129:D0WJDACXX:4:2308:5396:200008.1 /start=2 /end=100 /strand=+ Eukaryotic18S_rRNA
TTCTTAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGAGGGATGAACCTAACGTCGAG
TTAAGGTGCCTAACTATACGCTCATCAGATACCACAAAA

I would like to search the file and create new output files based on the different rRNA types. The six are Eukaryotic18S_rRNA Eukaryotic:28S_rRNA Bacterial:16S_rRNA Bacterial:23S_rRNA Archaeal:16S_rRNA Archaeal:23S_rRNA (note the missing : in Eukaryotic18S_rRNA is real, a mistake in the original program)

So a search for Bacterial:16S_rRNA would output to a different file

Code:
>HWI-ST766:129:D0WJDACXX:4:2308:5144:199799.1 /start=1 /end=85 /strand=- Bacterial:16S_rRNA
GGGGAGATCTCAAAGAGTCAGGTTGCTTGGAACTGCAGCCTTAAGCGGGAGATATGAAAC
TTCCAAAGCTAAATATAGATGGGAG
>HWI-ST766:129:D0WJDACXX:4:2308:4747:200053.1 /start=2 /end=96 /strand=+ Bacterial:16S_rRNA
AGATGACTCGCTGGACTTAAGCATATTATTAAGCGAAGGAAAAGAAATTAACAAAGATTG
CCTTAGTAAGGGCGACTGAACCGGCAATAGCTCGA

The input file could be searched serially for each key, or all at the same time, ouputing to different files. The input files are a few GB in size (but I do have a lot of memory).

Any help would be appreciated.
# 2  
Old 01-10-2013
try:
Code:
grep ">.*:.*[0-9]S_rRNA" infile | sed 's/.*[^0-9]\([0-9][0-9]*\)S_rRNA/\1S_rRNA/' | sort -u | while read rna
do
   awk -v rna="$rna" '
      BEGIN {s="^>.*" rna "$"; print s}
      $0 ~ s {p=1}
      $0 ~ /^>/ && $0 !~ s {p=0}
      p==1
   ' infile > "$rna.txt"
done
ls -l *.txt

# 3  
Old 01-10-2013
RE: Help: Parsing
Well that almost works. I did make a mistake in the input file. There are two more definitions that come up Bacterial:5S_rRNA and Eukaryotic:8S_rRNA. This leaves me to wonder whether there are others (such as Archaeal:5S_rRNA) that I had not considered in the input.

It also looks like the Archaeal:16S_rRNA and Bacterial:16S_rRNA end up in the same

16S_rRNA.txt output file.

Bob
# 4  
Old 01-10-2013
try version 1.1:
Code:
grep ">.* .*S_rRNA" infile | sed 's/ *$//; s/.* //' | sort -u | while read rna
do
   rm -f "$rna.txt"
   awk -v rna="$rna" '
      BEGIN {s="^>.*" rna "$";}
      $0 ~ s {p=1}
      $0 ~ /^>/ && $0 !~ s {p=0}
      p==1
   ' infile > "$rna.txt"
   ls -l "$rna.txt"
done

This User Gave Thanks to rdrtx1 For This Post:
fozrun
# 5  
Old 01-10-2013
Excellent! It looks like that does the job and outputs 9 result files.

Thanks!

Bob
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