
boro2013
New User
Jan 22, 2014, 10:37 AM
Post #2 of 3
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Re: [boro2013] Bioperl script help no programming skill at all
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so i managed to run the script now how do i add the files that i want and get the output....i need to know the correct way of adding the syntax i think....this is what it says ------------------------------------------- C:\Users\BL-pc>"C:\Perl\conversiontool.pl" Converts an alignment to another alignment format. C:\Perl\conversiontool.pl -i alignmentfile -o outputPrefix [-f outputformat] -i the alignment file to input -o the output alignment file or directory Specify a directory by a trailing slash. If a directory, the output format will be determined by -f. Default: fasta. -f output format possible values are derived from bioperl. e.g. fasta, clustalw, phylip, xmfa -g input format to force the correct input format, but it's ok to let it guess -c to concatenate the alignment into one solid entry -l linkerSequence, to be used with -c, to separate entries. Default is no linker but a useful linker could be NNNNNNNNNN -h this helpful menu at C:\Perl\conversiontool.pl line 19. C:\Users\BL-pc>"C:\Perl\conversiontool.pl""C:\Users\BL-pc\Desktop\mauve folder\f inal mauv\fm\assembled with run 3 and 4 L.f\run3 and 4 l.f"/"C:\Users\BL-pc\Desk top\mauve folder\final mauv\fm\assembled with run 3 and 4 L.f\New folder"[xmfa] The filename, directory name, or volume label syntax is incorrect. C:\Users\BL-pc>"C:\Perl\conversiontool.pl"-"C:\Users\BL-pc\Desktop\mauve folder\ final mauv\fm\assembled with run 3 and 4 L.f\run3 and 4 l.f"/"C:\Users\BL-pc\Des ktop\mauve folder\final mauv\fm\assembled with run 3 and 4 L.f\New folder"[xmfa] The filename, directory name, or volume label syntax is incorrect. C:\Users\BL-pc>"C:\Perl\conversiontool.pl"-"C:\Users\BL-pc\Desktop\mauve folder\ final mauv\fm\assembled with run 3 and 4 L.f\run3 and 4 l.f"/"C:\Users\BL-pc\Des
(This post was edited by boro2013 on Jan 22, 2014, 1:29 PM)
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