Nimble Perl Programming Using Scriptome

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Nimble Perl Programming Using Scriptome

• Yannick Pouliot, PhD
• Bioresearch Informationist
• Lane Medical Library Knowledge Management
  Center
• 1/22/2009

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Objectives

• Determining whether Scriptome can
• Enable you to perform operations otherwise
  difficult/time-consuming/error-prone?
• Help you learn Perl?

Also, well be using anonymous polling to
determine whether youre happy with the material
and speed of delivery
And dont worry This experiment wont hurt a bit!
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So What Is Scriptome?

• Scriptome is a resident Perl program that
  performs various data manipulation tasks useful
  to biologists
• Originally developed by Harvards FAS Center for
  Systems Biology
• Maintained and extended by lots more volunteers
  not associated with Harvard

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Why Bother With Scriptome?

• Code is visible, enabling learning on how to do
  things in Perl or not
• Can handle arbitrarily large files
• No size limitations, e.g., Excel
• Free runs on everything PC, Mac, Linux
• Its programmatic!
• Much faster than manual operations
• You can string operations together and save these
  in e.g. a .bat file

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How Do You Use Scriptome?

• You tell Scriptome which function you want it to
  perform (more later)
• You can also string Scriptome functions into a
  protocol
• Input Scriptome operates on text files
• No binary files, but you could add that
  capability yourself
• E.g., process Excel files in native form using
  Perl modules, e.g., ParseExcel
• Output command line or write into another file

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Scriptome Pick Your Flavor
http//lane.stanford.edu/howto/index.html?id_1257
http//sysbio.harvard.edu/csb/resources/computatio
nal/scriptome/
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Installing Scriptome - Windows

• Download Scriptome_exe.tar.gz using this link
  http//sysbio.harvard.edu/csb/resources/computatio
  nal/scriptome/bin/Scriptome_exe.tar.gz.
• ? Final location I suggest C/Program
  Files/Scriptome
• Create a directory named Scriptome
• Decompress Scriptome_exe.tar.gz by
  double-clicking
• ? Notice the four files inside
• Update the PATH variable
• add this string at the END of the contents of
  the PATH variable
• C\Program Files\Scriptome\ScriptomeC\Program
  Files\Scriptome\ScriptPackC\Program
  Files\Scriptome\Scriptome.batC\Program
  Files\Scriptome\ScriptPack.bat

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Scriptome Usage

• 1. Using a specific tool
• Scriptome flags toolname input_filenames gt
  output_filename
• Example
• Scriptome -t change_fasta_to_tab LONGhmcad.fst
• 2. Finding a tool by type
• Scriptome -t tooltype
• where tooltype
• Calc
• Choose
• Sort
• Fetch
• Merge
• Change
• Example
• Scriptome -t Calc

Lets examine each area briefly before going over
specifics
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Polling Time Hows the speed? 1 Too fast 2. Too
slow 3. More or less OK 4. I feel nauseous
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Examples and noteworthy tools
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Calc Tool Examples - 1

• Compute column sums
• Scriptome -t calc_col_sum SubjectData1.tab
• ? select columns to add
• IMPORTANT column numbers start at 0, not 1
• Note visible Perl code ? easy to modify, expand

perl -e " col1 while(ltgt) s/\r?\n//
_at_Fsplit /\t/, _ sum Fcol warn
qq\nSum of column col for . lines\n\n print
qqsum\n " file.tab
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Calc Tool Examples - 2

• Compute row sums
• Scriptome -t calc_row_sum SubjectData1.tab
• ? enter 1 for column 1, 2 for column 2, etc

perl -e " _at_cols(1, 2, 3) while(ltgt)
s/\r?\n// _at_Fsplit /\t/, _ sum 0
foreach col (_at_cols) sum Fcol
print qq_\tsum\n warn qq\nSum of
columns _at_cols for each line (. lines)\n\n "
in.tab
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Change Tool Examples - 1
perl -e " count0 len0 while(ltgt)
s/\r?\n// s/\t/ /g if (s/gt//) if
(. ! 1) print qq\n s/
/\t/ count _ . qq\t
else s/ //g len length(_)
print _ print qq\n warn qq\nConverted
count FASTA records in . lines to tabular
format\nTotal sequence length len\n\n "
seqs.fna

• Create tab-delimited file from FASTA file
• Scriptome -t change_fasta_to_tab LONGhmcad.fst gt
  LONGhmcad.fst.tab
• ? change_fasta_to_tab is an important tool
  because many Scriptome tools use tab-delimited
  files

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Change Tool Examples - 2

• Change rows to columns or vice versa
• Scriptome -t change_transpose_table
  SubjectData1.tab
• Note change_transpose_table operates on
  tab-delimited files

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Change Tool Examples - 3

• Create tab-delimited file from FASTA file
• Scriptome -t change_bio_format_to_bio_format
  LONGhmcad.fst
• enter fasta as input format (no quotes)
• enter genbank as output format (no quotes)
• change_bio_format_to_bio_format addresses the
  common problem of converting formats
• Important requires Bioperl to be installed

Notice anything interesting?
perl -MBioSeqIO -e " informat
qqgenbank outformat qqfasta count
0 for infile (_at_ARGV) in
BioSeqIO-gtnewFh(-file gt infile , -format gt
informat) out BioSeqIO-gtnewFh(-format
gt outformat) while (ltingt) print out
_ count warn qqTranslated
count sequences from informat to outformat
format\n " myseqs.genbank gt myseqs.fasta
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Conclusions

• Scriptome is
• A good solution for manipulating medium to large
  data files quickly and reliably
• A way to learn Perl in a real context (no toy
  problems)
• Able to perform a wide range of tasks, from
  simple, generic file manipulations to
  bio-specific complex tasks

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Resources

• For Perl help, see resources in workshop
  description in Lanes Perl Programming for
  Biologists
• Some recommended titles

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Polling Time Do you think Scriptome will be
useful to your research? 1. Definitely 2.
Likely 3. Not likely 4. No way 5. Whats the
question again?
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