Member Avatar for Anthony Cameron

When parsing an EMBL record (attached) do I follow the same directions as when I parse a GENBANK record? I have to print out the ID, KW, OC, and SQ fields once I parse the record. I have a code that would parse a GenBank record and would like to follow the same route if possible.

#!/usr/bin/perl
# Extract the annotation and sequence sections from the first
#  record of a GenBank library

use strict;
use warnings;
use BeginPerlBioinfo; 

# Declare and initialize variables
my $annotation = '';
my $dna = '';
my $record = '';
my $filename = 'sequence.gb';
my $save_input_separator = $/;

# Open GenBank library file
unless (open(GBFILE, $filename)) {
    print "Cannot open GenBank file \"$filename\"\n\n";
    exit;
}

# Set input separator to "//\n" and read in a record to a scalar
$/ = "//\n";

$record = <GBFILE>;

# reset input separator 
$/ = $save_input_separator;

# Now separate the annotation from the sequence data
($annotation, $dna) = ($record =~ /^(LOCUS.*ORIGIN\s*\n)(.*)\/\/\n/s);

# Print the two pieces, which should give us the same as the
#  original GenBank file, minus the // at the end
print $annotation, $dna;

exit;
ID   M91373; SV 1; linear; mRNA; STD; PLN; 1131 BP.
XX
AC   M91373;
XX
DT   24-APR-1992 (Rel. 31, Created)
DT   17-APR-2005 (Rel. 83, Last updated, Version 4)
XX
DE   Cucumis sativus peroxidase mRNA, complete cds.
XX
KW   peroxidase.
XX
OS   Cucumis sativus (cucumber)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   fabids; Cucurbitales; Cucurbitaceae; Cucumis.
XX
RN   [1]
RP   1-1131
RA   Rasmussen J.B., Smith J.A., Williams S., Burkhart W., Ward E.R.,
RA   Somerville S.C., Ryals J., Hammerschmidt R.;
RT   "Cloning and systemic expression of an acidic peroxidase associated with
RT   systemic acquired resistance to disease in cucumber";
RL   Unpublished.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1131
FT                   /organism="Cucumis sativus"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3659"
FT   sig_peptide     32..97
FT                   /gene="peroxidase"
FT                   /note="putative"
FT   CDS             32..1021
FT                   /codon_start=1
FT                   /gene="pre-peroxidase"
FT                   /product="peroxidase"
FT                   /note="putative"
FT                   /db_xref="GOA:Q39652"
FT                   /db_xref="HSSP:1PA2"
FT                   /db_xref="InterPro:IPR000823"
FT                   /db_xref="InterPro:IPR002016"
FT                   /db_xref="InterPro:IPR010255"
FT                   /db_xref="InterPro:IPR019793"
FT                   /db_xref="InterPro:IPR019794"
FT                   /db_xref="UniProtKB/TrEMBL:Q39652"
FT                   /protein_id="AAA33127.1"
FT                   /translation="MGLPKMAAIVVVVALMLSPSQAQLSPFFYATTCPQLPFVVLNVVA
FT                   QALQTDDRAAAKLIRLHFHDCFVNGCDGSILLVDVPGVIDSELNGPPNGGIQGMDIVDN
FT                   IKAAVESACPGVVSCADILAISSQISVFLSGGPIWVVPMGRKDSRIANRTGTSNLPGPS
FT                   ETLVGLKGKFKDQGLDSTDLVALSGAHTFGKSRCMFFSDRLINFNGTGRPDTTLDPIYR
FT                   EQLRRLCTTQQTRVNFDPVTPTRFDKTYYNNLISLRGLLQSDQELFSTPRADTTAIVKT
FT                   FAANERAFFKQFVKSMIKMGNLKPPPGIASEVRLDCKRVNPVRAYDVM"
FT   mat_peptide     98..1018
FT                   /gene="peroxidase"
FT                   /product="peroxidase"
FT                   /note="putative"
XX
SQ   Sequence 1131 BP; 314 A; 276 C; 229 G; 312 T; 0 other;
     accagagaag accccatttg cagtatcaaa aatgggttta cctaaaatgg cagccattgt        60
     tgtggtggtg gctttgatgc tatcaccctc tcaagcccag ctttctcctt tcttctacgc       120
     caccacatgc cctcagctgc ctttcgttgt tctcaacgtg gttgcccaag ccctacagac       180
     tgatgaccga gctgctgcta agctcattcg cctccatttt catgattgct ttgtcaatgg       240
     gtgtgatgga tcgattctat tggtagacgt accgggcgtt atcgatagtg aacttaatgg       300
     acctccaaat ggtggaatcc aaggaatgga cattgtggac aacatcaaag cagcagttga       360
     gagtgcttgt ccaggagttg tttcttgcgc tgatatctta gccatttcat ctcaaatctc       420
     tgttttcttg tcgggaggac caatttgggt tgtaccaatg ggaagaaaag acagcagaat       480
     agccaataga actggaacct caaacttacc tggtccctca gaaactctag tgggacttaa       540
     aggcaagttt aaagatcaag ggcttgattc tacagatctc gtggctctat caggagccca       600
     cacgtttgga aaatcaagat gcatgttctt cagtgaccgc ctcatcaact tcaacggcac       660
     aggaagaccc gacacaacgc ttgacccaat atacagggag cagcttcgaa gactttgtac       720
     tactcaacaa acacgagtaa atttcgaccc agtcacaccc actagatttg acaagaccta       780
     ttacaacaat ttgattagct taagagggct tctccaaagc gaccaagagc tcttctcaac       840
     tcccagagct gataccacag ccattgtcaa aacttttgct gccaacgaac gtgccttctt       900
     taaacaattt gtgaaatcaa tgatcaaaat gggcaacctc aagcctcccc ctggcattgc       960
     atcagaagtt agattggact gtaagagggt caacccagtc agagcctacg acgttatgta      1020
     ataactttat cccacttcat cccttctact tttgctgtct cttgtactac tttgttgatg      1080
     tattagttca accggttaag atatatatat cgttgaccta aataatagat c               1131
//
ID   M57705; SV 1; linear; mRNA; STD; ROD; 237 BP.
XX
AC   M57705;
XX
DT   05-APR-1991 (Rel. 28, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 3)
XX
DE   Rat truncated thyroid peroxidase mRNA, 3' end.
XX
KW   thyroid peroxidase.
XX
OS   Rattus norvegicus (Norway rat)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC   Muridae; Murinae; Rattus.
XX
RN   [1]
RP   1-237
RX   PUBMED; 2233737.
RA   Derwahl M., Seto P., Rapoport B.;
RT   "An abnormal splice donor site in one allele of the thyroid peroxidase gene
RT   in FRTL5 rat thyroid cells introduces a premature stop codon: association
RT   with the absence of functional enzymatic activity";
RL   Mol. Endocrinol. 4(6):793-799(1990).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..237
FT                   /organism="Rattus norvegicus"
FT                   /mol_type="mRNA"
FT                   /cell_type="FRTL5"
FT                   /db_xref="taxon:10116"
FT   exon            1..112
FT                   /partial
FT                   /gene="thyroid peroxidase"
FT                   /note="wild-type exon"
FT   CDS             1..142
FT                   /partial
FT                   /codon_start=2
FT                   /gene="thyroid peroxidase"
FT                   /product="truncated thyroid peroxidase"
FT                   /protein_id="AAA42250.1"
FT                   /translation="IDHDIALTPQSTSTAAFWGGVDCQLTCENQNPCFPIQILNGPKSR
FT                   K"
FT   variation       113
FT                   /gene="thyroid peroxidase"
FT                   /note="g in wt; a in truncated thyroid peroxidase gene.
FT                   This changes a splice donor site to a readthrough
FT                   sequence."
FT   intron          113..167
FT                   /gene="thyroid peroxidase"
FT                   /note="wild-type intron"
FT   exon            168..237
FT                   /partial
FT                   /gene="thyroid peroxidase"
FT                   /note="wild-type exon"
XX
SQ   Sequence 237 BP; 56 A; 87 C; 45 G; 49 T; 0 other;
     catcgatcat gacattgctc tcacaccaca gagcaccagc acagcagcct tctggggagg        60
     tgtcgactgc cagttgacct gtgagaacca aaacccctgc ttccccatac agattctaaa       120
     tggacccaag agccgaaagt gacatccagt ctcccccttt gccacagctt ccctcaaact       180
     cctcacggac cactgcatgc ctacctttct accgctcctc agccgcctgt ggcactg          237
//
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  • 3 Days Discussion Span
  • Latest Post Latest Post by Anthony Cameron
Member Avatar for d5e5

I really don't know the bioinformatics subject matter involved here. I tried changing the regex and adding a chomp statement because including the newline \n in my regex caused it to fail on my computer for some reason. Here is what I changed:

# Now separate the annotation from the sequence data
#($annotation, $dna) = ($record =~ /^(LOCUS.*ORIGIN\s*\n)(.*)\/\/\n/s);#GenBank layout
($annotation, $dna) = ($record =~ /^(.*SQ\s*)(.*)\/\//s);#Trying to matchEMBL layout
chomp($annotation, $dna);
Member Avatar for Anthony Cameron

I really don't know the bioinformatics subject matter involved here. I tried changing the regex and adding a chomp statement because including the newline \n in my regex caused it to fail on my computer for some reason. Here is what I changed:

# Now separate the annotation from the sequence data
#($annotation, $dna) = ($record =~ /^(LOCUS.*ORIGIN\s*\n)(.*)\/\/\n/s);#GenBank layout
($annotation, $dna) = ($record =~ /^(.*SQ\s*)(.*)\/\//s);#Trying to matchEMBL layout
chomp($annotation, $dna);

Okay, I manipulated the script with the addition and I got the entire record. In order for me to get the specific data I want should I just input them when I declare my variables? Thanks

Member Avatar for Anthony Cameron

I really don't know the bioinformatics subject matter involved here. I tried changing the regex and adding a chomp statement because including the newline \n in my regex caused it to fail on my computer for some reason. Here is what I changed:

# Now separate the annotation from the sequence data
#($annotation, $dna) = ($record =~ /^(LOCUS.*ORIGIN\s*\n)(.*)\/\/\n/s);#GenBank layout
($annotation, $dna) = ($record =~ /^(.*SQ\s*)(.*)\/\//s);#Trying to matchEMBL layout
chomp($annotation, $dna);

Hi, since I need to pring out the $ID, $SQ, $KW, AND $OC within the file should I declare them as variables and then print them out? Thanks

Member Avatar for d5e5

Hi, since I need to pring out the $ID, $SQ, $KW, AND $OC within the file should I declare them as variables and then print them out? Thanks

Why declare four scalar variables just to store the four literal values you want to look for at the beginning of the lines? Also, I don't know why you want to follow the same route as illustrated in the script you posted. That script reads two mult-line records into two variables: $annotation and $dna, which it then prints. Why do that if what you really want is to print the lines from the file that begin with ID, SQ, KW, or OC?

Why not take the following approach?

  1. Read the file one line at a time
  2. Test each line to see if it begins with ID, SQ, KW, or OC
  3. Decide whether or not to print the line based on the result of the test?

Maybe I don't understand what you mean by 'parsing' the file but it seems to me that a simple script like the following does what you say you want to do:

#!/usr/bin/perl
#embl01.pl
use strict;
use warnings;

my $filename = '/home/david/Programming/data/EMBL_records.txt';

open my $fh, $filename or die "Could not open $filename: $!";

while (<$fh>){
    chomp;
    if (m/^(ID|SQ|KW|OC)/){#Does line start with ID, SQ, KW, or OC?
        print $_, "\n";
    }
}

This gives the following output:

ID   M91373; SV 1; linear; mRNA; STD; PLN; 1131 BP.
KW   peroxidase.
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   fabids; Cucurbitales; Cucurbitaceae; Cucumis.
SQ   Sequence 1131 BP; 314 A; 276 C; 229 G; 312 T; 0 other;
ID   M57705; SV 1; linear; mRNA; STD; ROD; 237 BP.
KW   thyroid peroxidase.
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC   Muridae; Murinae; Rattus.
SQ   Sequence 237 BP; 56 A; 87 C; 45 G; 49 T; 0 other;
Member Avatar for Anthony Cameron

Why declare four scalar variables just to store the four literal values you want to look for at the beginning of the lines? Also, I don't know why you want to follow the same route as illustrated in the script you posted. That script reads two mult-line records into two variables: $annotation and $dna, which it then prints. Why do that if what you really want is to print the lines from the file that begin with ID, SQ, KW, or OC?

Why not take the following approach?

  1. Read the file one line at a time
  2. Test each line to see if it begins with ID, SQ, KW, or OC
  3. Decide whether or not to print the line based on the result of the test?

Maybe I don't understand what you mean by 'parsing' the file but it seems to me that a simple script like the following does what you say you want to do:

#!/usr/bin/perl
#embl01.pl
use strict;
use warnings;

my $filename = '/home/david/Programming/data/EMBL_records.txt';

open my $fh, $filename or die "Could not open $filename: $!";

while (<$fh>){
    chomp;
    if (m/^(ID|SQ|KW|OC)/){#Does line start with ID, SQ, KW, or OC?
        print $_, "\n";
    }
}

This gives the following output:

ID   M91373; SV 1; linear; mRNA; STD; PLN; 1131 BP.
KW   peroxidase.
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   fabids; Cucurbitales; Cucurbitaceae; Cucumis.
SQ   Sequence 1131 BP; 314 A; 276 C; 229 G; 312 T; 0 other;
ID   M57705; SV 1; linear; mRNA; STD; ROD; 237 BP.
KW   thyroid peroxidase.
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC   Muridae; Murinae; Rattus.
SQ   Sequence 237 BP; 56 A; 87 C; 45 G; 49 T; 0 other;

Thank you for your response and I guess I should not have tried to follow the same procedure as the one posted. I simply needed to retrieve the four pieces of information and use a subroutine. I think that I was confusing the procedures because I wanted to use a subroutine from BeginPerlBioinfo.

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