def fasta_subset(infileName, outfileName, ids) :
if type(ids) != type({}) :
import misc
ids = misc.list2dict(ids)
outfile = open(outfileName, 'w')
for rec in fasta_itr(infileName) :
if rec.header in ids :
outfile.write(str(rec))
def extractLines(fileName, lines) :
'''extract the lines given by a list of line numbers in the file'''
file = open(fileName)
lineDict = misc.list2dict(lines)
lineNum = 1
for line in file :
if lineNum in lineDict :
print line[:-1]
lineNum += 1
file.close()
def selectLines(infile, outfile, lines, keepLines = 1) :
'''write to outfile the lines in infile whose line number is in the
given list of line numbers'''
infileHandle = open(infile)
outfileHandle = open(outfile, 'w')
lineDict = misc.list2dict(lines)
lineNum = 0
for line in infileHandle :
lineNum += 1
if keepLines == 1 :
if lineNum in lineDict :
outfileHandle.write(line)
else :
if lineNum not in lineDict :
outfileHandle.write(line)
