Readme file for formatter.py 26th Dec 2002

Usage

This python script is meant for the production of other types of output not provided by the program MGAlign. The program MGAlign 
must be run such that the second type of output. This output is then piped into formatter.py for the production of other types of 
output. This is shown below:

mgalign -g genomic_sequence_file -m mRNA_sequence_file -o 2 | formatter.py -o 1

For help on the usage of MGAlign, read the program's readme file. Formatter.py has only one option "-o". The number after this 
option specifies the output format. Current formatter.py outputs 3 different types of output. 

The first ouput type ("-o 1") shows the various exons as individual FASTA formatted sequence. The header line of each FASTA file  
shows the exon number, the type of sequence (mRNA or genomic), the filename of the sequence, the start position (starting from 
0), the ending position, the number of matches, the number of mismatches and the number of gaps.

The second output type ("-o 2") shows the alignment as two FASTA formatted sequence. The first being the mRNA sequence and the 
second being the genomic sequence. The header line of each FASTA file shows the type of sequence (mRNA or genomic), the start 
position (starting from 0) and the end position.

The third output type ("-o 3") shows the intron sequences as individual FASTA formatted sequence. The header line of each 
sequence shows the intron number, whether it is sense or anti-sense, the filename, the start position (starting from 0), the end 
position and the length of the intron.

As it is a python script, it is very easy to change, just open the file and make the necessary changes. Just ensure that the 
first line points to the python interpreter. The output format of MGAlign is very easy to parse, so you can parse it in other 
computer languages (you can even use the unix tool "cut"). See the readme for MGAlign for details of the format it outputs.

Contact

Any comments or suggestions are greatly appreciated. You can forward them to Bernett Lee at bernett@bic.nus.edu.sg