Friday, August 05, 2005

get rid of ^A ^B in emacs ipython shell

add in .emacs:
(add-hook 'comint-mode-hook
'(lambda ()
(add-hook 'comint-output-filter-functions
'shell-filter-ctrl-a-ctrl-b nil t)))
(defun shell-filter-ctrl-a-ctrl-b (string)
"Remove `^A' and `^B' characters from comint output.
These characters may show up in the prompt of bash, due to a bug in
bash. If you experience this problem, put this function in
`comint-output-filter-functions'."
(let ((pmark (process-mark (get-buffer-process (current-buffer)))))
(save-excursion
(goto-char (or comint-last-output-start (point-min)))
(while (re-search-forward "[\C-a\C-b]" pmark t)
(replace-match "")))))

Thursday, May 26, 2005

vmatch commands

mkvtree

mkvtree -db file -pl -allout -dna -indexname filename.index

Overview of the mkvtree-Options
-db specify database files (mandatory)
-q specify query files
-smap specify file containing a symbol mapping
-dna input is DNA sequence
-protein input is Protein sequence
-indexname specify name for index to be generated
-pl specify prefix length for bucket sort
-rev use reverse input sequence
-tis output transformed input sequences (tistab) to file
-ois output original input sequences (oistab) to file
-suf output suffix array (suftab) to file
-sti1 output reduced inverse suffix array (sti1tab) to file
-bwt output Burrows-Wheeler Transformation (bwttab) to file
-bck output bucket boundaries (bcktab) to file
-lcp output longest common prefix lengths (lcptab) to file
-skp output skip values (skptab) to file
-allout output all index tables to files
-v verbose mode
-help this option


Overview of the vmatch-Options sorted by Categories
Input parameter
-q specify files containing queries to be matched
Kind of matches
-tandem compute right branching tandem repeats
-supermax compute supermaximal matches
-mum compute maximal unique matches
-complete specify that query sequences must match completely
Postprocessing of matches
-dbnomatch mask all database substrings containing a match
-qnomatch show all query substrings not containing a match
-dbmaskmatch mask all database substrings containing a match
-qmaskmatch mask all query substrings containing a match
-dbcluster cluster the database sequences
-nonredundant generate file with non-redundant set of sequences;
-selfun specify shared object file containing selection function
-dbms specify values for connecting to a database
Algorithms
-online run algorithms online without using the index
-qspeedup specify speedup level when matching queries
Direction of matches
-d compute direct matches (default)
-p compute palindromic (i.e. reverse complemented matches)
Match constraints
-l specify that match must have the given length
-h specify the allowed hamming distance > 0
-e specify the allowed edit distance > 0
-allmax show all maximal matches in the order of their computation
-seedlength specify the seed length
-hxdrop specify the xdrop value for hamming distance extension
-exdrop specify the xdrop value for edit distance extension
-leastscore specify the minimum score of a match
-evalue specify the maximum E-value of a match
-identity specify minimum identity of match in range [1..100%]
Output modes
-sort sort the matches, additional argument is mode
-best show the best matches (those with smallest E-values)
-i give information about number of different matches
Output formats
-s show the alignment of matching sequences
-showdesc show sequence description of match
-f show filename where match occurs
-absolute show absolute positions
-nodist do not show distance of match
-noevalue do not show E-value of match
-noscore do not show score of match
-noidentity do not show identity of match

Wednesday, May 25, 2005

reverse string in PYTHON

reversed_string = string_to_reverse[::-1]

or

reversed_string = ''.join(reversed(string_to_reverse))