SC rate Version 1.1 Introduction Example sc_rate.pl test_sequence_align.msf or sc_rate.pl test_sequence_align.msf test_struct_align.saln Contact jong@mrc-lmb.cam.ac.uk Warranty I will do my best to fix. Copyright GPL #________________________________________________________________________ # Title : sc_rate.pl (or sc_rate in certain cases) # Usage : sc_rate.pl test_file.msf [test_structure_file.jp] # Function : Evaluates the quality of any sequence alignment. # This caculates, basically, the Sequence identity(in %) divided # by Composition identity rate of sequences with certain scanning # window size of (8 ~ 24) # Example : sc_rate.pl aa.msf aa.jp # Warning : Takes 'ALIGNED' sequences. So, need at least a pair of seqs aligned. # Class : Bio # Keywords : SC rate, Sequence identity, composition identity # Options : Following vars are read into the program at initialization by &parse_arguments # subroutine, so please leave them. It is not just comments. # $av_sc_segment becomes 1 by a # To smooth the SC rates # SC rates with Window size defined by a=X . # $make_gap_dot becomes d by d # Modifies SC rate by a dynamic factor of window # $av_sc_segment = [ ] by a= # window size for averaging after getting SC rates # $show_calculation becomes s by s # Shows the scanning windows during calculation # $no_stat becomes ns by ns # do not show stat with 2 file inputs( # $variable_win_size becomes v by v # This sets the scan win size dynamic # $output_ordered becomes o by o # in final printing, seq # $interlaced_out becomes i by i # in final printing, seq # $normal_sc_rate becomes n by n # Normalize (0-9) the SC rates # $normal_er_rate becomes e by e # Normalize (0-9) the error rates(2 file input) # $conv_err_2_bin becomes c by c # Converts error rates to 0 or 1 (occurred or not) # $redu_window becomes r by r # Tries to reduce the scan wind # This is only activated with 'v' option. # $apply_factor becomes f by f # Modifies SC rate by a dynamic factor of window # size. This is only activated with 'v' option # $minus_whole_cs becomes m by m # substracts rates with whole seq # # this makes rates more strict in predicting # $print_width_size is [ ] by w= # the final output print block width # # $ss_opt becomes ss by ss, SS, -ss, -SS # for secondary structure only # $H = 'H' by -H or -h or H or h # to retrieve only H segment # $S becomes 'S' by -S or S # to retrieve only S segment # $E becomes 'E' by -E or E # to retrieve only E segment # $T becomes 'T' by -T or -t or T or t # to retrieve only T segment # $I becomes 'I' by -I or I # to retrieve only I segment # $G becomes 'G' by -G or -g or G or g # to retrieve only G segment # $B becomes 'B' by -B or -b or B or b # to retrieve only B segment # $HELP becomes 1 by -help # for showing help # $simplify becomes 1 by -p or P or -P, p # $simplify becomes 1 by -simplify or simplify, Simplify SIMPLIFY # $comm_col becomes 'C' by -C or C or common # $LIMIT becomes L by -L, L # to limit the error rate to 9 . # $HELP becomes 1 by -h, h, '?' # for showing help # Package : # Reference : # Returns : No file writing. # Tips : This is handy to see how reliable your alignment is. # Argument : Upto 2 files and various options (in '-h' or 'h' format ) # Todo : # Author : A Biomatic # Version : 1.1 # Used in : Bio # Enclosed : #--------------------------------------------------------------------