python regex- getting everything (except \n) between two characters in a multiline string -

-

i have file input:

>x0 cuugacgauca cgcaucg >x55 uacggcgg uucagc aucg >x300 aaacccgggg

and need concatenation of lines between '>' characters: 

cuugacgaucacgcaucg uacggcgguucagcaucg aaacccgggg

my attempt use "re.match(r'^>.*\n(.*)>.*' ,a,re.dotall)" , delete '\n' each match, regex not returning anything. wrong?

some people, when confronted problem, think "i know, i'll use regular expressions." have 2 problems. - jamie zawinski

that being said, why not more understandable string processing?

tmp = [] seqs = [] open('txtfile') f:     line in f:         if line.startswith('>'):             seqs.append(''.join(tmp))             tmp = []         else:             tmp.append(line.strip())     else:         seqs.pop(0)         seqs.append(''.join(tmp))

alternatively, if want use regex, try first stripping newlines , splitting >x[digit] patterns:

re.split(r'>x\d+', re.sub(r'\n', '', data))

but has downside entire textfile has loaded variable data, not interesting large file (which in bio-informatics quite common). then, approach given first more interesting, memory-wise, process each finished dna/rna-sequence in turn.


Comments

Post a Comment

Popular posts from this blog

python - mat is not a numerical tuple : openCV error -

-
i have write down code showing error ma not getting it: please help: showing mat not numerical tuple: import cv import cv2 capture = cv2.videocapture("j.3gp") while(1): _, frame1 = capture.read() grayimage1 = cv2.cvtcolor(frame1, cv2.color_bgr2gray) _, frame2 = capture.read() grayimage2 = cv2.cvtcolor(frame2, cv2.color_bgr2gray) differenceimage = cv2.absdiff(grayimage1,grayimage2) thresholdimage = cv2.threshold(differenceimage,25,255,cv2.thresh_binary) cv2.imshow("difference image", differenceimage) cv2.imshow("threshold image", thresholdimage) cv2.imshow("image", frame1) k = cv2.waitkey(30) & 0xff error arising : ----------------------------------------------------------------------------------------- traceback (most recent call last): file "desk.py", line 15, in <module> cv2.imshow("threshold image", thresholdimage) typeerror: mat not numerical tuple ...
Read more

c# - MSAA finds controls UI Automation doesn't -

-
i'm working on automating windows application. i'm using teststack white framework. i've hit problem. program has 'window' object cannot see inside of. white shows no controls inside of it. inspect.exe shows no controls inside of either when running in ui automation mode. if switch inspect msaa see controls inside fine. there anyway me use msaa c# handle on these controls? if can identify msaa functions need, can use p/invoke call them c#. here's example article doing msaa: http://www.codeproject.com/articles/38906/ui-automation-using-microsoft-active-accessibility also, pinvoke.net can used identify iaccessible (msaa) functions: http://www.pinvoke.net/search.aspx?search=iaccessible&namespace=[all] here's answer along lines: msaa com-based? finally, alternative p/invoke, might able use tlbimp.exe create wrapper assembly oleacc.dll, , access msaa functions through it. i'm not sure if works msaa, it's worth try. as e...
Read more

wordpress - .htaccess: RewriteRule: bad flag delimiters -

-
pulling hair out on one. have following .htaccess file custom redirects in addition wordpress's default settings. when tested on local wamp server worked fine after moving production i'm not getting rewriterule: bad flag delimiters error in server log , after while site goes down internal server error any appreciated. in advance! <ifmodule mod_rewrite.c> rewriteengine on rewritebase / rewriterule ^rockford_weddings___welcome\.html$ /wedding/ [r=301,l] rewriterule ^blog/?$ /journal/ [r=301,l] rewriterule ^blog/(.*)$ /$1 [r=301,l] rewriterule ^portraitinvestment/?$ /portraitinvestment\.pdf [r=301,l] rewriterule ^weddinginvestment/?$ /weddinginvestment\.pdf [r=301,l] rewriterule ^holidaycards2014/?$ /holidaycards2014\.pdf [r=301,l] </ifmodule> # begin wordpress <ifmodule mod_rewrite.c> rewriteengine on rewritebase / rewriterule ^index\.php$ - [l] rewritecond %{request_filename} !-f rewritecond %{request_filename} !-d rewriterule . /index.php [l] </...
Read more