Mercurial > repos > yating-l > regtools_junctions_extract

annotate validator.py @ 1:06d9062f5430 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 93217f9e3a1bc1afc8ce971176e4ae0169a8f265
author sargentl
date Wed, 28 Nov 2018 14:20:39 -0500
parents 01ed8e112f2a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
1 import sys
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
2
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
3 """
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
4 Call checkAndFixBed, check the integrity of bed file. If the strand is not "+" or "-" truncate that line and report to users
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
5 create a column and move the score column to that column.
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
6 """
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
7 def checkAndFixBed(bedfile, revised_file):
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
8 # Store the lines that have been removed
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
9 removedLines = []
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
10 # Remove the lines with invalid strand, create a score column to store the original scores and change scores in the original score column all to 1000
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
11 with open(revised_file, 'w') as tmp:
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
12 with open(bedfile, 'r') as f:
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
13 lines = f.readlines()
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
14 i = 1
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
15 for line in lines:
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
16 fields = line.split()
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
17 strand = fields[5]
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
18 score = fields[4]
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
19 fields[4] = '1000'
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
20 fields.append(score)
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
21 if (strand == '+' or strand == '-'):
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
22 tmp.write('\t'.join(map(str, fields)))
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
23 tmp.write("\n")
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
24 else:
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
25 removedLines.append("line" + str(i) + ": " + line)
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
26 i = i+1
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
27
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
28 return removedLines
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
29
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
30 def main():
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
31 inputfile = str(sys.argv[1])
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
32 outputfile = str(sys.argv[2])
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
33 removed = checkAndFixBed(inputfile, outputfile)
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
34 if (removed != []):
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
35 print "\nRemoved invalid lines: \n"
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
36 print "\n".join(removed)
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
37
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
38 if __name__ == "__main__":
01ed8e112f2a planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
yating-l
parents:
diff changeset
39 main()