Not every script is optimized for speed and is likely to be improved over time.
RUN_A_SITE_ANALYSIS.PY, visualize the amino acid distributions of reads around the open reading frame of genes
usage: run_a_site_analysis.py --sam SAM --gff GFF --fa FA [--nc NC] [--nb NB] [--mq MQ] [--o53 O53] [--o35 O35] [--title TITLE] [--log] [--op OP] [--ow] [--orf] [--csv] [--verbose] [--lim LIM] [-h]
options:
--sam SAM (str, required) the input sam(or bam) file
--gff GFF (str, required) the file with gene definitions
--fa FA (str, required) the file with nucleotide sequences
--nc NC (int, default=1) the number of cores to use
--nb NB (int, default=1) the number of blocks to use (NC<=NB)
--mq MQ (int, default=41) the minimum mapping quality of a read
--o53 O53 (int, default=14) the offset from 5->3 direction
--o35 O35 (int, default=12) the offset from 3->5 direction
--title TITLE (str, default=) the sample title
--log (bool, default=False) write output to a log file
--op OP (str, default=) output folder, if not specified same as folder where sam resides
--orf (bool, default=False) generate ORF plots
--csv (bool, default=False) export plot data to csv file
--verbose: (bool, default=False) # show extra logging information, useful for debugging
--lim (float, default=0.8) # set memory limit, throws error if exceeded
-h, --help show this help message and exit
usage: alt_predict_v2.py --input_file INPUT_FILE --fasta_file FASTA_FILE [--gff_file GFF_FILE] [--nt_upstream NT_UPSTREAM] [--nt_downstream NT_DOWNSTREAM] [--min_hits MIN_HITS] [--down_offset DOWN_OFFSET] [--up_offset UP_OFFSET] [--min_qual MIN_QUAL] [--nlines NLINES] [-h]
options:
--input_file INPUT_FILE (str, required) the input file (only sam files).
--fasta_file FASTA_FILE (str, required) the fasta file to generate sequences for motif detection.
--gff_file GFF_FILE (str, default=) optional, if supplied the peaks are annnotated with the location on the genome e.g. gene, ORF of gene.
--nt_upstream NT_UPSTREAM (int, default=50) the number of positions upstream (towards 5') from the first nt of the A-site.
--nt_downstream NT_DOWNSTREAM (int, default=48) the number of positions downstream (towards 3') from the first nt of the A-site.
--min_hits MIN_HITS (int, default=1) pauses should have at least min_hits reads.
--down_offset DOWN_OFFSET (int, default=12) the offset when read from the 3' end.
--up_offset UP_OFFSET (int, default=14) the offset when read from the 5' end.
--min_qual MIN_QUAL (int, default=42) the minimum mapping quality of the reads.
--nlines NLINES (int, default=1_000_000) the number of lines to be processed in a single block.
-h, --help show this help message and exit.