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Bioperl script help no programming skill at all

boro2013
New User

Jan 22, 2014, 9:55 AM

Post #1 of 3 (2183 views)

Bioperl script help no programming skill at all	Can't Post

Hi
Iv got a file in XMFL format (obtained using Mauve) and i want to convert it into multifasta format.
Iv got a script that would do that and iv installed active perl with bioperl and i want to know what i need to change/or add to have my file converted ( and whether i paste the script on to cmd).

the script can be obtained from: http://www.bioperl.org/wiki/Converting_alignment_files

help would be greatly appreciated as iv been trying to figure this out for 2 days
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(This post was edited by boro2013 on Jan 22, 2014, 1:31 PM)

boro2013
New User

Jan 22, 2014, 10:37 AM

Post #2 of 3 (2179 views)

Re: [boro2013] Bioperl script help no programming skill at all [In reply to]	Can't Post

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

In Reply To

(This post was edited by boro2013 on Jan 22, 2014, 1:29 PM)

Laurent_R
Veteran / Moderator

Jan 22, 2014, 1:47 PM

Post #3 of 3 (2162 views)

Re: [boro2013] Bioperl script help no programming skill at all [In reply to]	Can't Post

I have trouble understanding what you are looking for, but it seems quite clearly that you need to launch your program with a command similar to this:

Code

C:\Users\BL-pc>C:\Perl\conversiontool.pl -i input_file -o output_file

where "input_file" is the path and the name of the input file, and "output_file" the path and the name of the output file. So try to do it the way it is recommended to do it, possibly something like this:

Code

C:\Perl\conversiontool.pl -i C:\Users\BL-pc\Desktop\mauve folder\final mauv\fm\assembled -o C:\Users\BL-pc\Desktop\the_file_you_want_to_generate

You might have trouble, though, with the fact that two of the directory names have spaces in them. Either you can try this:

Code

C:\Perl\conversiontool.pl -i "C:\Users\BL-pc\Desktop\mauve folder\final mauv\fm\assembled" -o C:\Users\BL-pc\Desktop\the_file_you_want_to_generate

or, if that still does not work, you move your input file into a directory where the path has no directory_name with spaces in it, for example something like this:

Code

C:\Perl\conversiontool.pl -i C:\Users\BL-pc\Desktop\mauve_folder\final_mauv\fm\assembled" -o C:\Users\BL-pc\Desktop\the_file_you_want_to_generate

I hope this helps, but if this is not sufficient, please try to explain more clearly what you need, what you did, what output you obtained and in which way it is not what you want.

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