GenBank Files

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GenBank Files
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GenBank Files

• Arrays vs. Scalars
• Using the input separator variable /
• Using offsets to control file access

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GenBank Files

• Beginning Perl for Bioinformatics
• O'Reilly web site has online resources for this
  book http//perl.oreilly.com/
• Download Examples and Exercises
• Be sure to get the module BeginPerlBioinfo.pm

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GenBank Files

• In order to use the sub's inside
  BeginPerlBioinfo.pm, you need to include this
  line in your code
• use BeginPerlBioinfo
• assumes the module is in the same directory
  as the perl code that uses the module.
  Otherwise, you need to use the command
• use lib 'path/to/lib'

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GenBank Files

• Parsing a file arrays vs. scalars
• Each has its advantages and disadvantages
• Arrays
• each line is an element
• useful if each line is processed the same way
• not so useful when info you want spans multiple
  lines

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GenBank Files

• Parsing a file arrays vs. scalars
• Scalars
• entire file is a scalar
• useful when info you want spans multiple lines
• info extracted with regular expressions

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GenBank Files

• Parsing a file as an array chronological order
• if(at_beginning)
• keep going
• elsif(in_middle)
• extract_info
• elsif(at_end)
• finish_up

This order seems logical but it doesn't work
well.
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GenBank Files

• Parsing a file as an array use reverse
  chronological order
• if(at_end)
• finish up
• elsif(in_middle)
• extract_info
• elsif(at_beginning)
• keep going

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GenBank Files

• !/usr/bin/perl -w example 10-1
• use strict
• use BeginPerlBioinfo
• my _at_annotation ( )
• my sequence ''
• my filename 'record.gb'
• parse1(\_at_annotation, \sequence, filename)
• print _at_annotation
• print_sequence(sequence, 50)
• exit

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GenBank Files

• sub parse1
• my(annotation, dna, filename) _at__
• annotation-reference to array
• dna -reference to scalar
• filename -scalar
• declare and initialize variables
• my in_sequence 0
• my _at_GenBankFile ( )
• Get the GenBank data into an array from a
  file
• _at_GenBankFile get_file_data(filename)

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GenBank Files

• foreach my line (_at_GenBankFile)
• if( line /\/\/\n/ )
• last break out of the foreach loop.
• elsif( in_sequence) flag true
• dna . line
• elsif ( line /ORIGIN/ )
• in_sequence 1 set the flag.
• else otherwise
• push( _at_annotation, line)
• dna s/\s0-9//g strip whitespace
• and numbers

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GenBank Files

• sub parse1
• note no return value
• references to variables declared in main are
  passed into sub
• values are added to references to variables in
  main, therefore no need to return anything
• sub call
• parse1(\_at_annotation, \sequence, filename)

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GenBank Files

• Parsing a GenBank file as a scalar
• Entire record is a scalar
• Extract info with regular expressions

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GenBank Files

• sub get_annotation_and_dna
• my(record) _at__ ltlt GenBank file as
  scalar
• my(ann) ''
• my(dna) ''
• (ann, dna) (record /(LOCUS.ORIGIN\s\n)(
  .)\/\/\n/s)
• dna s/\s\///g
• return(annotation, dna)

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GenBank Files

• Using regular expressions to match multiline
  scalars
• pattern modifiers /s and /m
• file /pattern1(.)pattern2/s
• /s allows the . to match any character
  including newline character(\n)
• /s does NOT affect the anchors and

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GenBank Files

• Using regular expressions to match multiline
  scalars
• pattern modifiers /s and /m
• file /pattern1(.)pattern2/m
• /m allows the . to match any character
  including newline character(\n) AND permits pat
  to match
• \npat in a multiline scalar
• /m affects the and anchors /s does not

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GenBank Files

• How we think of files
• my list
• cat
• horse
• mouse
• car
• house

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GenBank Files

• How a computer thinks of a file
• my list \ncat\nhorse\nmouse\ncar\nhouse(eof)
• file /horse.ar/s no match
• file /horse.ar/m MATCH

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GenBank Files

• Using regular expressions to extract information
  from the GenBank File
• Accession
• DNA Sequence
• Protein Sequence
• Gene
• Organism

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GenBank Files

• Using regular expressions to grab the Accession
  number from file
• ACCESSION BC013459
• sub get_accession
• my GB_file shift
• if(GB_file/ACCESSION\s(\w)/)
• return 1
• else
• return 'error'

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GenBank Files

• Using regular expressions to grab the Gene name
  from file
• /gene"Bmp4"
• sub get_gene
• my GB_file shift
• if(GB_file/gene"(.?)"/s)
• return 1
• else
• return 'unknown'

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GenBank Files

• Using regular expressions to grab the DNA
  sequence from file
• ORIGIN
• 1 gagagggtgg tgctggaggg tgggaaggca
  agagcgcgag
• ...
• 1741 tggactttta tcttaaaaaa aaaaaaaaaa aaaaaa
• //

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GenBank Files

• Using regular expressions to grab the DNA
  sequence from file
• sub get_dna_sequence
• my GB_file shift
• my seq
• if(GB_file/ORIGIN\s(.)\/\//s)
• seq 1
• else
• return "error"
• seq s/\s\d//g
• return uc(seq)

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GenBank Files

• Using regular expressions to grab the protein
  sequence from file
• /translation"MIPGNRMLMVVLLCQVLLGGASHASLIPETGKKK
  VAEIQGHAGG
• RRSGQSHELLRDFEATLLQMFGLRRRPQPSKSAVIPDYMRDLYRLQSG
  EEEEEEQSQG
• TGLEYPERPASRANTVRSFHHEEHLENIPGTSESSAFRFLFNLSSIPE
  NEVISSAELR
• LFREQVDQGPDWEQGFHRINIYEVMKPPAEMVPGHLITRLLDTRLVHH
  NVTRWETFDV
• SPAVLRWTREKQPNYGLAIEVTHLHQTRTHQGQHVRISRSLPQGSGDW
  AQLRPLLVTF
• GHDGRGHTLTRRRAKRSPKHHPQRSRKKNKNCRRHSLYVDFSDVGWND
  WIVAPPGYQA
• FYCHGDCPFPLADHLNSTNHAIVQTLVNSVNSSIPKACCVPTELSAIS
  MLYLDEYDKV
• VLKNYQEMVVEGCGCR"

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GenBank Files

• Using regular expressions to grab the protein
  sequence from file
• sub get_protein_sequence
• my GB_file shift
• my pro
• if(GB_file/translation"(.?)"/s)
• pro 1
• else
• return "error"
• pro s/\s//g
• return uc(pro)