I am writing a program to compare two different files.
For each line in file1 i want to compare it to all the lines in file2, then go to the next line in file1.
the code i have below is not looping back to the next line in file1, can anyone give me any suggestions to help?
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#! /usr/bin/env python
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import sys
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import fileinput
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# Open the two files
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f1 = open(sys.argv[1], "r")
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f2 = open(sys.argv[2], "r")
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for line in f1:
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chrR,chrStart,chrEnd,name,score,strand1,codingStart,codingEnd,itemRbg,blockCount,blockSize,BlockStart = line.strip().split()
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chr = range(int(chrStart), int(chrEnd))
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lncRNA = set(chr)
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for line in f2:
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chrC,clustStart,clustEnd,annote,score,strand = line.strip().split()
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clust = range(int(clustStart), int(clustEnd))
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cluster = set(clust)
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if strand1 == '-':
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if chrR == chrC:
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if strand1 == strand:
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if lncRNA & cluster:
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print name, annote, 'transcript'
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else:
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continue
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continue
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break
