gpuFFTMSA
GPU accelerated FFT-based multiple sequence alinger.
Requirements:
For the CPU portion of the code to work, only python, numpy, pylab(for debug) need to be installed.
For GPU portion, the above need to be available, as well as pyCUDA and pyFFT.CUDA
Usage:
- if pyFFTalign.py is run without arguments it will gather default values out of ./data
usage: pyFFTalign.py [-h] [-i INPUT_GENOME] [-s INPUT_SEQS]
[--logFile LOGFILE] [-l LOGLEVEL] [-g] [-e] [--verify]
given a directory of input genomes and sequences it will try to match up each
sequence to its genome
optional arguments:
-h, --help show this help message and exit
-i INPUT_GENOME, --inputgenome INPUT_GENOME
Input genome file or dir of fna files (Default:
./data/sampleGenome.fna)
-s INPUT_SEQS, --inputseqs INPUT_SEQS
Input sequence file (Default: ./data/sampleGenome.seq)
--logFile LOGFILE output to log file (Default: False)
-l LOGLEVEL, --log LOGLEVEL
Log level, use DEBUG of more output (Default: INFO)
-g, --usegpu gpu option (Default: False)
-e, --chopefficient chop efficiently (Default: False)
--verify verify successfull transcription (Default: False)
Note: input files are expected in the following format
*.fna => INPUT_GENOME:
>some title
ATATTTTTTCTTGTTTTTTATATCCACAAACTCTTTTCGTACTTTTACACAGTATATCGTGTTGTGGACA
ATTTTATTCCACAAGGTATTGATTTTGTGGATAACTTTCTTAATTTCATTGCTATAGCTACTTTTTTTTG
ATATTATAGTTGTGTTTTCACTTTGAATAAGTTTTCCACATCTTTATCTTATCCACAATTTGTGTATAAC
ATGTGGACAGTTTTAATCACATGTGGGTAAATGATTATCCACATTTGCTTTTTTGTCGAAAACCCTATCT
*.seq => INPUT_SEQS:
some title|ATATTATAGTTGTGTTTTCACTTTGAATAAGTTTTCCACATCTTTATCTTATCCACAATTTGTGTATAAC
Code layout:
- pyFFTalign.py
- Provides basic command-line parsing and provides a wrapper for the other two.
- Reads in Genome(long sequence)
- Reads in Sequences(shorter sequences)
- dataObj.py
- Data container for raw and transcribed sequences
- transcribes sequences on object creation
- methods for returning padded raw and transcribed sequences
- aligner.py
- CPU and GPU correlation functions