Awesome

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DESCRIPTION

maptools package contains a number of lift-over, alignment, and sequence retrieval tools.

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INSTALLATION

To install, type './configure' to cofigure and 'make all' to compile all the binaries

============================================================================ UTILITIES

Sequence compressing/decompressing/retrieval

transf: this utility transforms fasta files (usually, genomes) into an indexed 4-bit format, with 2 bits encoding ACGT and the other two encoding Ns and repeat masked state

./transf -dir <dirname> -maskdir <dirname> -dbx <file> -idx <file> [-remove] [-uncompress] [-quiet]
-dir name of the directory containing FASTA files
-maskdir name of the directory containing masked FASTA files (optional)
-maskext masked FASTA file extension
-dbx, -idx sequence database names
-remove remove source FASTA files [default=NO]
-uncompress [default=NO]
-quiet suppress verbose output [default=NO]

Examples:
./transf -dir human_genome/file.fa -dbx hg19.dbx -idx hg19.idx
Creates hg19.dbx and hg19.idx from all files in human_genome/
./transf -dir human_genome/file.fa -dbx hg19.dbx -idx hg19.idx -uncompress
Creates human_genome/* from hg19.dbx and hg19.idx

getsegm: this utility does sequence retrieval from the 4-bit repository (see transf) given the input file of intervals

./getsegm -in <file> -dbx <file> -idx <file> -out <file> [-limit <length>] [-margins <margin1> <margin2>] [-quiet] 
-in BED file (NOTE: although the columns are as in BED file, the coordinate system is 1-based!)
 -dbx, -idx database files
-out output file
-limit [default=800000] sequence length limit (if the length of the interval is greater than this limit, 
nucleotides in the middle are replaced by the spacer)
-spacer [default=.....]
-margins <margin1> <margin2> [default=0 0] margins to add on each side of the interval

getwind: this utility does sequence retrieval from the 4-bit repository (see transf) given the input file of positions and window sizes

./getwind -in <file> -dbx <file> -idx <file> -out <file>
-we exonic window [default=0] -wi intronic window [default=150] -cis [use colunms 1-3] [default=4207174]
-quiet <suppress verbose output> [default=no]
-all <include all sites>
-coord <offset for acceptor sites> [default=0]

Lift-over and mapping utilities

map_agnostic: this utility does liftOver of nucleotide coordinates (cps format) by using chain alignment.

./map_agnostic -in <cps_file> -chain <chain_alignment_file> -out <output_file> [-margin <margin>] [-quiet]
-in chromosome/position/strand tab-delimited file (strand is +/-), has to be sorted by position in ascending order
-chain chain_alignment_file (see UCSC genome browser)
-out <output_file> [default=stdout]
-margin margin length [default=0]
-quiet suppress verbose output [default=NO]

Input format: chromosome1/position1/strand1; chain species 1=>2
Output format: chromosome1/position1/strand1/chromosome2/position2/strand2/chain_id

map_single: same as map_agnostic, but also takes into account gene information specified in column 4 of cps

Input format: chromosome1/position1/strand1; chain species 1=>2
Output format: chromosome1/position1/strand1/chromosome2/position2/strand2/gene/site/type/score

syntenic_filter: this utility takes a non-unique mapping in cps3+cps3 format and does ad-hoc filtering of the projected coordinates by maximum synteny genome-wide

./syntenic_filter -in <aln_file> -out <output_file> [-maxdepth <int>] [-threshold <double>] [-lendiff <diff>] [-quiet]
-in cps3+cps3 file, remember to sort by position in ascending order
-out <output_file> [default=stdout]
-maxdepth <integer> how many preceding positions can be skipped [default=4]
-threshold <double> max change of segment length, in percent [default=1.50]
-lendiff <integer>, [default=100000]
-quiet suppress verbose output [default=NO]
Note: the mapping [x,x+dx] -> [y,y+dy] is OK if |dy-dx|/dx<threshold OR |dy-dx|<dlimit

best_match: same as syntenic_filter but takes cps3+cps6 output of map_single and looks for maximum synteny PER GENE

net_filter: currently deprecated but still retained in the package.

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