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.:: Aminoacid Composition::.
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Amico version 0.7 |
Description
Amico is a PHP script which identifies a given amino acid composition on the first "n" residues of an aminoacid fasta (sigle/multiple) sequence file.Amico identifies all sequences found to meet the following criteria:
P+S = 11 & A+V<=8
Althought this criteria is hard-coded in the script itself, it can be modified to meet your own needs (I forgot to mention it? It's Open Source:-) via the "searchCriteria" function.
Algorythm
- Reads an Input file
- Save each aminoacid sequence in an array field
- Remove fasta header from the sequence
- Check if sequence has an appropriate minimum length
- Cut the first n residues
- Search for criteria
- Write results
Output
Amico outputs a short report to the STDOUT, and creates a directory on the same directory from where it was launched.For instance, if you run Amico as:
$> amico myFastaFile.fasta
It creates the following directory structure:
amico-myFastaFile.fasta/ |__failLength.csv |__failCriteria.csv |__results.csv
And does the same for each file you run, so your results will have their own directory, and you can run multiple analysis on the same root directory.
- failLength.csv: lists all the sequences which didn't meet the "minimum length requirement as to be analyzed (for instance if you want to check for a given aminoacid composition on the first 50 residues you might define that sequence must be at least 100 residues long.
- failCriteria.csv: lists all sequences that didn't meet the search criteria.
- results.csv:lists the sequences which met criteria with its residues composition.
As you can see, results are formatted in Comma Separated Values (CSV), so you can open them in any software which supports it (Calc or excel).
Usage
As for this Amico version the only command line option supported (and required) is your query file. No other option is supported, so parameters should be set in the script itself (probably the variables you'll want to modify are $MINLEN and $CUTSIZE).Depending on your system configuration you can run amico in any of the following ways:
$> php amico yourFastaFile
For the following option to work the amico script must have the execution flag turned on:
$> chmod +x amico
$> ./amico yourFastaFile
$> ./amico yourFastaFile