python - Selecting specific lists in a file -


i've been working python dictionary replace md5 values cog/nog identifiers. have done far...

#!/usr/bin/python  import sys  fil = sys.argv[1]  # load md5 -> cog dictionary  open(fil) fin:      rows = ( line.strip().split('\t') line in fin )     d = { row[0]:row[1] row in rows }  # open blast output, replace md5 cog looking md5 in dictionary      blasted = open(sys.argv[2])     line in blasted:             linearr = line.split()             if linearr[2] > '90.00':                     line.split()                     needed = linearr[0:2]                     md5 = linearr[1]                                                     ret = []                     md5 in needed:                             ret.append(d.get(md5,md5))                             "".join(ret)                             print ret

this has brought me output, lists of various size , content...

['fig|357276.26.peg.4486'] ['fig|357276.26.peg.4486', 'f3e68ef307f962ba6b836a94ff0e2216'] ['fig|357276.26.peg.4486'] ['fig|357276.26.peg.4486', 'cog0860'] ['fig|357276.26.peg.4486'] ['fig|357276.26.peg.4486', '05e94199eef6fbaf225618f9deaf847c']

so single item lists need tossed lists retain md5 value. need select lists have cog/nog second element, in 4th list above.

i can't select second item of lists filter these results because not lists have second item. can suggest method this?

update: able remove lists 1 item. lists this...

['fig|357276.26.peg.4485', 'nog73961'] ['fig|357276.26.peg.4485', '19c060b530e8fa9598de068387bc3225'] ['fig|357276.26.peg.4486', '8daa25fe83eb1a204c51861cb77945f5'] ['fig|357276.26.peg.4486', '5c253078a0a6c51eca320dfd92991a70'] ['fig|357276.26.peg.4486', '8707bd7fa7489ff69233ce735c1c6cbf'] ['fig|357276.26.peg.4486', 'f3e68ef307f962ba6b836a94ff0e2216'] ['fig|357276.26.peg.4486', 'cog0860'] ['fig|357276.26.peg.4486', '05e94199eef6fbaf225618f9deaf847c']

now need select lists containing second item starting nog or cog...any advice?

lets have list of lists values = [ [1], [1,2], [3,4] ]

first remove items filter function:

values1 = filter(lambda x: len(x) > 1, values)

now need filter based on cog/nog. there lists 2 elements now, can directly choose second element :

filter(lambda x: "nog" in x[1] of "cog" in x[1], values1)

to reduce whole thing down, can merge both:

def check_cog_nog(x):     if len(x) > 1:         y = x[1].lower()         if "nog" in y or "cog" in y:             return true     return false  filter(check_cog_nog, values)

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