Difference between revisions of "GBrowse syn Scripts"
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:Use this script in cases where you have a one or more clustal alignment files and want to convert them to the [[GBrowse_syn_Database#alignment_data_loading_format|tab-delimited format]] that is used to load the GBrowse_syn alignment database. | :Use this script in cases where you have a one or more clustal alignment files and want to convert them to the [[GBrowse_syn_Database#alignment_data_loading_format|tab-delimited format]] that is used to load the GBrowse_syn alignment database. | ||
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| − | + | :This script is deprecated. You can use the [[GBrowse_syn_Scripts#load_alignments_msa.pl|load_alignments_msa.pl]] to load the database directly. | |
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Revision as of 19:51, 12 December 2009
This page describes helper scripts for processing alignment data for loading into GBrowse_syn.
Contents
Parsing Multiple Sequence Alignment Data
The scripts in this section process multiple sequence alignment data in various formats and convert them to the tab-delimited format used to load the GBrowse_syn database.
aln2hit.pl
aln2hit.pl is a generic alignment data parser that reads alignment data into the GBrowse_syn database loading format.
- Purpose
- Use this script in cases where you have a single alignment file and want to convert it to the tab-delimited format that is used to load the GBrowse_syn alignment database.
- Note
- This script is deprecated. You can use the load_alignments_msa.pl to load the database directly.
- Example
perl aln2hit.pl -f clustalw -i my_alignments.aln >my_alignments.txt
- Options
| argument | default | description |
|---|---|---|
| f | clustalw | Specifies the alignment file format. Most common formats recongnized by BioPerl's AlignIO parsers are supported. Use clustalw or fasta for best results. |
| i | Specifies the name of the input alignment file |
clustal2hit.pl
clustal2hit.pl is a CLUSTALW format alignment data parser.
- Purpose
- Use this script in cases where you have a one or more clustal alignment files and want to convert them to the tab-delimited format that is used to load the GBrowse_syn alignment database.
- Note
- This script is deprecated. You can use the load_alignments_msa.pl to load the database directly.
- Example
perl clustal2hit.pl *.aln >my_alignments.txt
- Options
None.
mercatoraln_to_synhits.pl
mercatoraln_to_synhits.pl is a data parser for multiple sequence alignments generated by mercator.
- Purpose
- This script will process alignments generated by the MERCATOR pipeline
- Example
Usage example here
- Options
| argument | default | description |
|---|---|---|
| a | output.mfa | Specifies the name of the alignment file |
| v | Print progress reports while running | |
| f | fasta | Specifies format of the input alignment files |
| d | Specifies the containing directory for the genome and map files |
Direct Database Loading Scripts
The scripts in this section load data from multiple sequence alignment files into the GBrowse_syn alignment database
load_alignment_database.pl
- Purpose
- This script loads the alignment database from a tab-delimited alignment data files (format described here).
- Example
perl load_alignment_database
| argument | default | description |
|---|---|---|
load_alignments_gff3.pl
| argument | default | description |
|---|---|---|
load_alignments_msa.pl
| argument | default | description |
|---|---|---|
