a wrapper for finding alignments using bowtie2
To align a fasta file:
./fasta_align.py ignyta_0.8_gsp1.fasta
where 'ignyta_0.8_gsp1.fasta' is the name of the fasta you want to align. The './' means 'run this file'.
Additionally, you can specify the '-a' flag to print all alignments, not just those with multiple hits.
./fasta_align.py -a ignyta_0.8_gsp1.fasta
To align a sequence:
./sequence_align.py CCATCCTCCTCCTTTTCCTCCTCCC