Hello,
I am using this package on Windows 7 64bit
http://gnuwin32.sourceforge.net/packages/pcre.htm (in the specific instance I used pcre-7.0.exe available here
http://sourceforge.net/projects/gnuwin32/files/pcre/7.0/ to have pcregrep available on my Windows machine).
That is to say:
pcregrep version 4.4 29-Nov-2006 using PCRE version 7.0 18-Dec-2006
When I use this line from the Windows command prompt
pcregrep -vM "^>sp\|.{6}\-.\|.*\n(.*\n\w)*" PIG.fasta > PIG_without_isoforms.fasta
I have nothing done (no errors, it simply looks like that nothing is happening, the command does not stop and an empty output file is produced).
When I use this line (the only changes with respect to the previous one are double quotes to single quotes)
pcregrep -vM '^>sp\|.{6}\-.\|.*\n(.*\n\w)*' PIG.fasta > PIG_without_isoforms.fasta
on Unix (pcregrep version 7.8 2008-09-05) everything works.
The above line (the one with double quotes) works in Windows if I replace -vM with -v
The above line (the one with double quotes) works in Windows if I replace -vM with -M
It seems that the combination of options -vM affects Windows.
I'd like to update pcregrep to the latest version (pcre is at version 8.31) but I have no idea (see note below) on how to do that without a precompiled Windows port like the above mentioned one or without a step-by-step protocol.
Could you help me in trying to update pcregrep on my Windows system?
I'd very much like to be able to do what can be done on Unix also on Windows (like it happens for all the other GnuWin32 packages that I use).
PLEASE NOTE: I am not an informatics expert but just a simple user.
The compressed version of the input file (if you would like to perform tests) is available here:
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/PIG.fasta.gz
Thanking you in advance for your kind attention
Best Regards
Emanuele Alpi
