bed2fasta-http

#!/usr/bin/gawk -f

BEGIN { 
    db = "";
    db = ARGV[1];
    if (db=="") {
        print "no database name specified for bed2fasta! -h for help." > "/dev/stderr";
        noend=1
        exit(1);
    }
    if (db=="-h") {
        print "bed2fasta-http: get fasta sequence from given assembly (parameter 1) for given regions (bed from stdin) with a dumb and simple wget request to UCSC.";
        print "remember to sleep enough between requests, UCSC is unhappy otherwise";
        noend=1
        exit;
        }

    c = 0;
    ARGV[1]="-"

    }

/^track/ { next }
/^#/ {next}

// { 
    split($0, fields)
    seq = fields[1];
    begin = fields[2];
    end = fields[3];
    strand="-"
    if (length(fields)>3) {
        name=fields[4];
        score=fields[5];
        strand=substr(fields[6],1,1);
        }
    else {
        strand="+";
    }
    print "Downloading " seq ":" begin "-" end "/" strand > "/dev/stderr";
    system("fastaFromUCSC " seq " " begin " " end " " db " "strand"");
    c+=1;
}

END { if (noend=0) { 
    print "Got " c " sequences, check the results! (invalid coords will lead to wrong sequence)" > "/dev/stderr" ; }
}