GenBank Files and Libraries

1
GenBank Files and Libraries
2
GenBank Files and Libraries

• GenBank records have defined structure making it
  easy to parse the desired information with
  regular expressions
• GenBank Libraries are files that contain many
  individual GenBank records
• For instance the GenBank Library of human RNA has
  28,158 records

3
GenBank Files and Libraries

• Methods for processing large files
• The input separator variable /
• Using offsets to control file access

4
GenBank Files and Libraries

• The input separator variable /
• By default this input separator is set to \n
• When a file is fed into an array, each element is
  split on the \n character
• _at_array ltFHgt

5
GenBank Files and Libraries

• The input separator does not have to be \n
• You can set this variable in order to split a
  file however you like
• For instance, GenBank libraries have many
  individual records
• Suppose you want to create an array where each
  element is a GenBank record from a library

6
GenBank Files and Libraries

• sub get_next_record
• my(fh) _at__ filehandle stored in
  fh
• my(record) ''
• my(save_input_separator) /
• / "//\n"
• record ltfhgt
• / save_input_separator restore /
• return record

7
GenBank Files and Libraries

• Using the get_next_record sub
• while(record get_next_record(fh))
• push(_at_records, record)

8
GenBank Files and Libraries

• Using the input separator variable /
• Essentially, this is the same as collecting a
  file into a scalar and then using the split
  command
• library get_file(fh)
• _at_records split(/\/\/\n/, library)

9
GenBank Files and Libraries

• Using the file offset to control file reading
• perl keeps track of where it is while reading a
  file
• similar to how it keeps track of where it is
  during pattern matching

10
GenBank Files and Libraries

• Offsets
• You can get access to the offset value by using
  the tell function
• offset tell(filehandle)
• The offset value can be very useful when using
  very large files (like GenBank libraries)

11
GenBank Files and Libraries

• example10-8.pl
• processes a GenBank library using an array of
  records
• array was made using input separator
• each GenBank record was parsed to save Accession
  and offset
• DBM file was written with key accession and
  value offset
• allows rapid access to individual records in the
  file without having to scroll through the whole
  file

12
GenBank Files and Libraries

• !/usr/bin/perl
• Example 10-8 - make a DBM index of a GenBank
  library,
• and demonstrate its use interactively
• use strict
• use warnings
• use BeginPerlBioinfo see Chapter 6 about
  this module

13
GenBank Files and Libraries

• Declare and initialize variables
• my fh
• my record
• my dna
• my annotation
• my fields
• my dbm
• my answer
• my offset
• my library 'library.gb'

14
GenBank Files and Libraries

• open DBM file, creating if necessary
• unless(dbmopen(dbm, 'GB', 0644))
• print "Cannot open DBM file GB with mode
  0644\n"
• exit

15
GenBank Files and Libraries

• Parse GenBank library, saving accession number
  and
• offset in DBM file
• open file and save filehandle in fh
• fh open_file(library)
• get offset ltlt should start at 0
• offset tell(fh)

16
GenBank Files and Libraries

• while ( record get_next_record(fh) )
• (annotation, dna) get_annotation_and_dna(
  record)
• fields parse_annotation(annotation)
• my accession fields'ACCESSION'
• extract just the accession number from the
  accession
• field and remove any trailing spaces
• accession s/ACCESSION\s//
• accession s/\s//
• store the key/value of accession/offset
• dbmaccession offset
• get offset for next record
• offset tell(fh)

17
GenBank Files and Libraries

• print "Here are the available accession
  numbers\n"
• print join ( "\n", keys dbm ), "\n"
• print "Enter accession number (or quit) "
• This was written for library with 5 records
• Not a great plan for one with thousands

18
GenBank Files and Libraries

• while( answer ltSTDINgt )
• chomp answer
• if(answer /\sq/)
• last
• offset dbmanswer
• if (defined offset)
• seek(fh, offset, 0) ltltltltlt seek
  uses offset
• record get_next_record(fh)
• print record
• else

19
GenBank Files and Libraries

• else
• print "Do not have an entry for
  answer\n"
• print "\nEnter accession number (or quit) "

20
GenBank Files and Libraries

• seek function
• seek (FH, offset, 0)
• This positions the pointer to this FH at the
  offset value
• The 3rd argument is for 'WHENCE'
• 0 offset read from start
• 1 offset read from current position
• 2 offset read from end (negative offset
  expected)

21
GenBank Files and Libraries

• LOCUS AB031069 2487 bp mRNA
  PRI 27-MAY-2000
• DEFINITION Homo sapiens PCCX1 mRNA for protein
  containing CXXC domain 1,
• complete cds.
• ACCESSION AB031069
• VERSION AB031069.1 GI8100074
• KEYWORDS .
• SOURCE Homo sapiens embryo male lung
  fibroblast cell_lineHuS-L12 cDNA to
• mRNA.
• ORGANISM Homo sapiens
• Eukaryota Metazoa Chordata
  Craniata Vertebrata Euteleostomi
• Mammalia Eutheria Primates
  Catarrhini Hominidae Homo.
• REFERENCE 1 (sites)
• AUTHORS Fujino,T., Hasegawa,M., Shibata,S.,
  Kishimoto,T., Imai,Si. and
• Takano,T.
• TITLE PCCX1, a novel DNA-binding protein
  with PHD finger and CXXC domain,
• is regulated by proteolysis
• JOURNAL Biochem. Biophys. Res. Commun. 271
  (2), 305-310 (2000)

22
GenBank Files and Libraries
LOCUS AB031069 2487 bp mRNA
PRI 27-MAY-2000 DEFINITION Homo sapiens
PCCX1 mRNA for protein containing CXXC domain 1,
complete cds. ACCESSION
AB031069 VERSION AB031069.1
GI8100074 KEYWORDS . SOURCE Homo sapiens
embryo male lung fibroblast cell_lineHuS-L12
cDNA to mRNA. ORGANISM Homo
sapiens Eukaryota Metazoa Chordata
Craniata Vertebrata Euteleostomi
Mammalia Eutheria Primates Catarrhini
Hominidae Homo. REFERENCE 1 (sites) AUTHORS
Fujino,T., Hasegawa,M., Shibata,S.,
Kishimoto,T., Imai,Si. and Takano,T.
TITLE PCCX1, a novel DNA-binding protein
with PHD finger and CXXC domain, is
regulated by proteolysis JOURNAL Biochem.
Biophys. Res. Commun. 271 (2), 305-310 (2000)
23
GenBank Files and Libraries
LOCUS AB031069 2487 bp mRNA
PRI 27-MAY-2000 DEFINITION Homo sapiens
PCCX1 mRNA for protein containing CXXC domain 1,
complete cds. ACCESSION
AB031069 VERSION AB031069.1
GI8100074 KEYWORDS . SOURCE Homo sapiens
embryo male lung fibroblast cell_lineHuS-L12
cDNA to mRNA. ORGANISM Homo
sapiens Eukaryota Metazoa Chordata
Craniata Vertebrata Euteleostomi
Mammalia Eutheria Primates Catarrhini
Hominidae Homo. REFERENCE 1 (sites) AUTHORS
Fujino,T., Hasegawa,M., Shibata,S.,
Kishimoto,T., Imai,Si. and Takano,T.
TITLE PCCX1, a novel DNA-binding protein
with PHD finger and CXXC domain, is
regulated by proteolysis JOURNAL Biochem.
Biophys. Res. Commun. 271 (2), 305-310 (2000)
24
GenBank Files and Libraries

• example10-8.pl
• processes a GenBank library using an array of
  records
• array was made using input separator
• each GenBank record was parsed to save Accession
  and offset
• DBM file was written with key accession and
  value offset
• allows rapid access to individual records in the
  file without having to scroll through the whole
  file