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Full Discussion: Help: Parsing a file to new output files
Top Forums Shell Programming and Scripting Help: Parsing a file to new output files Post 302754363 by fozrun on Thursday 10th of January 2013 01:06:57 PM
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.
 

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LEARN ABOUT MINIX

ppmtosixel

ppmtosixel(1)                                                 General Commands Manual                                                ppmtosixel(1)

NAME

       ppmtosixel - convert a portable pixmap into DEC sixel format

SYNOPSIS

       ppmtosixel [-raw] [-margin] [ppmfile]

DESCRIPTION

       Reads  a  portable  pixmap  as input.  Produces sixel commands (SIX) as output.  The output is formatted for color printing, e.g. for a DEC
       LJ250 color inkjet printer.

       If RGB values from the PPM file do not have maxval=100, the RGB values are rescaled.  A printer control header and a color assignment table
       begin the SIX file.  Image data is written in a compressed format by default.  A printer control footer ends the image file.

OPTIONS

       -raw   If  specified,  each  pixel  will  be explicitly described in the image file.  If -raw is not specified, output will default to com-
              pressed format in which identical adjacent pixels are replaced by "repeat pixel" commands.  A raw file is often an order  of  magni-
              tude larger than a compressed file and prints much slower.

       -margin
              If  -margin  is not specified, the image will be start at the left margin (of the window, paper, or whatever).  If -margin is speci-
              fied, a 1.5 inch left margin will offset the image.

PRINTING

       Generally, sixel files must reach the printer unfiltered.  Use the lpr -x option or cat filename > /dev/tty0?.

BUGS

       Upon rescaling, truncation of the least significant bits of RGB values may result in poor color conversion.  If the original PPM maxval was
       greater  than  100,  rescaling  also reduces the image depth.  While the actual RGB values from the ppm file are more or less retained, the
       color palette of the LJ250 may not match the colors on your screen.  This seems to be a printer limitation.

SEE ALSO

       ppm(5)

AUTHOR

       Copyright (C) 1991 by Rick Vinci.

                                                                   26 April 1991                                                     ppmtosixel(1)
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