bioLegato Online Help

Open and Import Files

The bioLegato File --> Open menu is "hardwired" into bioLegato, and can open the main file types that are intrinsic to the bioLegato program: GDE (.gde), GenBank (.gen), FASTA (.fsa) and flat (.flat). Each bioLegato interface also has one or more Import menus, which have been programmed for data types that are specific to each bioLegato interface.

The Open Menu

The File --> Open menu will only read files in GDE (.gde), FASTA (.fsa), GenBank (.gen), or flatfile (.flat) format.

GenBank format - bioLegato can read any file in GenBank format, as defined in the GenBank release notes from NCBI [ ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt]. Files originally-read in GenBank format can also be saved as GenBank files, because biolegato stores the annotation portion of each GenBank entry as text, unchanged from the original file.

One word of caution is in order regarding saving in GenBank format. If a sequence was read in a different format (eg. FASTA) bioLegato will save in a pseudo-GenBank format, in which only minimal annotation fields are written, since the data for complete annotation does not exist in most other file formats.  using File --> SaveAs. However, this format loses some of the annotation information from the original GenBank file, and in other cases, rearranges data, so that GenBank files generated by bioLegato do NOT comply with the official standard.

Examples:
thionin.gen - file containing two thionin sequences directly retrieved from NCBI.
thionin.biolegato.gen - thionin.gen was read into bioLegato and then saved using SaveAs.
Warning: Although the differences between these two formats may look minor, they may break programs that read GenBank files. Therefore, when retrieving GenBank files using biolegato or dbiolegato, it is best to save them directly to a file, rather than sending them to biolegato and later saving.


GDE format - This format is similar to the ASN.1 format used in databases. It preserves most of the annotation from the original GenBank file.

Example:
thionin.gde - thionin.gen was read into biolegato and then saved using SaveAs.

GDE flatfile format - This is a minimal format, which only retains the name and sequence data. It is used by biolegato to create temporary files, and there is no way to directly save to this format.

Example:
thionin.flat - bioLegato flat file using thionin sequences from above.

The name of each "sequence" in a GDE flat file indicates the type of data:
# - DNA/RNA
% - protein
@ - mask sequence
" - text

For example, a bioLegato flat file containing a list of GI numbers for DNA sequences from Brassica insularis (TaxID 69183) might look like this:

"69183.dna.gi
75707982,57638973,57638879,44888690,9719214,2598264,2598263

bldna,blprotein,blnalign, blpalign

The File --> Import Foreign Format menu calls readseq, which can translate a number of sequence formats into a pseudo-GenBank format. The ouput is then read into biolegato. It is important to realize that no other file format contains the complete information found in GenBank files. Usually, only the name of the sequence and the sequence itself are retained. Even if this function is used to read in a GenBank file, the fact that it is processed by both readseq and biolegato means that the full annotation may not be retained.
Note on circular sequences: The only common sequence file format that can specify whether a sequence is circular or linear is GenBank. Always use this format when working with circular sequences.


SaveAs


The SaveAs menu can be used to save in any of the four formats supported by biolegato.

Export Foreign Format


The File --> Export Foreign Format menu also calls readseq, to create files in numerous formats. Again, since biolegato can not necessarily export all of the original annotation, some annotation my not appear in the exported files.

Example:
thionin.fasta - Fasta-format file using thionin sequences from above.


bltable

Todo: add documentation for bltable

blmarker

blmarker works with discrete state data, such as molecular markers. The File --> Import Phylip Discrete Data menu translates a Phylip discrete data file into biolegato flat file, and imports the flat file.

Example:
manitoba.phyl - set of 13 RAPD markers

Similarly, the File --> Export Phylip Discrete Data menu saves discrete state data as a flat file, which is then translated into a Phylip discrete data file.








Importing Data from a Spreadsheet

Molecular marker data is often assembled in a spreadsheet, as illustrated below. Marker data for each species, isolate, or strain should be in a row. The first column is holds tha name of the species, isolate or strain, and the remaining columns have the marker data, such that each column is a different marker (ie. locus).


To use this data in blmarker, it must be saved as a Comma-Separated Value file (.csv).

If you are using StarOffice or OpenOffice Calc,
 If you are using Microsoft Excel

For example, if your spreadsheet file was MarkerExample.xls, then save your data to MarkerExample.csv.
At this point it is a good idea to check your .csv file by looking at it in a text editor. It should look something like this:

"LR27        ",0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,1,0,1,1,1,1,0,0,0,1,1,1,1,1,1,1
"LR29           ",0,0,0,0,0,0,0,0,1,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,0,0,1,1,1,1,1,1,1
"LR210          ",1,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,1,0,1,0,0,0,0,0,1,0,1,0,1,1,0,0,1,0,0,0,0,0,0,1,1,0,1,0,1,1,1,1,0,1,0,0,1,0,0,1,1,1,1
"LR211          ",1,0,1,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,1,1,1,0,1,0,0,1,1,0,1,1,1,0,0,1,0,0,0,0,0,0,1,0,0,1,1,1,1,0,1,0,1,1,1,1,0,1,1,1,1,1
"LR212          ",1,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,1,0,1,0,0,0,0,0,1,0,1,0,1,1,0,0,1,0,0,0,0,0,0,1,0,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
"LR213          ",1,1,0,0,0,1,1,0,0,0,0,0,0,0,1,1,0,0,1,1,1,1,0,1,0,1,1,0,1,1,1,1,1,1,0,1,1,1,1,1,1,1,0,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
"LR214          ",0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0,1,0,0,1,0,0,1,1,1,0,0,0,0
"LR215          ",0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,0,0,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1,0,1,1,1,1,1,1,0,1,0,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1
"LR216          ",1,0,1,1,0,1,0,0,1,1,0,0,0,1,0,0,1,1,1,0,1,0,1,1,1,1,1,0,1,1,1,1,0,1,0,0,0,0,0,0,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1
"LR217          ",0,1,0,0,0,1,0,0,0,0,0,0,0,0,1,1,0,0,1,1,1,1,1,1,0,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
"LR218          ",0,0,1,0,1,0,1,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0,1,0,0,1,1,1,0,0,0,1,0,1,0,0,0,0,0,0,0,1,1,0,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1
"LR219          ",1,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,1,0,1,1,1,0,0,0,0,0,0,0,0,0,1,1,0,0,1,1,0,1,0,1,1,1,1,1,1,1,1,1,1
"LR220          ",1,0,1,1,0,0,0,0,1,0,0,0,0,1,0,0,1,1,0,0,0,0,0,1,1,1,0,0,1,1,1,1,0,1,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1

Note: The example above shows that the name field is enclosed in quotes. These are okay, as quotes will be automatically stripped out when the file is read by blmarker.
To import this file into blmarker, choose File --> Import Discrete Data from CSV file.

The .csv file is read into blmarker, which should appear as shown below.

Note: you could also convert a .csv file into a Phylip file at the Unix command line using csv2phyl.sh.




bltree


bltree works with phylogenetic trees. The File --> Import Treefile menu translates a Phylip treefile into biolegato flat text file, and imports the flat file.

Example:
sample.treefile - file containing 3 trees

Similarly, the File --> Export Treefile menu saves trees in a flat text file, which is then translated into a Phylip treefile.