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recallSpots.py bug

PBHoney Tickets
Nick Booher
2014-06-19
2015-03-26

  • Nick Booher

    Nick Booher - 2014-06-19

    recallSpots.py in PBSuite_14.5.1 gives this error:

    Traceback (most recent call last):
  File "/opt/PBSuite_14.5.13/bin/recallSpots.py", line 27, in <module>
    if spot.tags["label"] == "INS" and filterINSZ(container, bam, spot, args):
TypeError: filterINSZ() takes exactly 3 arguments (4 given)

    Copying stuff over from HSpots.py seems to fix it:

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    #!/usr/bin/env python

import sys, logging, argparse
import pysam
from pbsuite.honey.HSpots import *
from pbsuite.utils.setupLogging import setupLogging
USAGE = "Recall spots in a hon.h5 file"

args = parseArgs(sys.argv[1:], established=True)

setupLogging(args.debug)

f = h5py.File(args.hon,'a')
bam = pysam.Samfile(args.bam)
tsp = 0
makeKernals(args.binsize)
print "#CHROM\tOUTERSTART\tSTART\tINNERSTART\tINNEREND\tEND\tOUTEREND\tINFO"
for chrom in f.keys():
    logging.info("Calling %s" % (chrom))
    container = f[chrom]["data"]
    spots = callHotSpots(container, f[chrom].attrs["start"], args)
    logging.info("Filtering INSZ Spots")
    fspot = 0
    for spot in spots:
        spot.chrom = chrom
        #add tags for pval and container stats etc
        spot.offset(f[chrom].attrs["start"])

        if spot.tags["label"] == "INS" and filterINSZ(bam, spot, args):
            continue
        if (spot.size < args.sizeMin or spot.size == -1) or spot.size > args.sizeMax:
            continue
        fspot += 1 
        print spot
    tsp += fspot
    logging.info("Found %d spots" % (fspot))
logging.info("Finished %d spots" % (tsp))
     

  • Adam English

    Adam English - 2014-06-19

    Hey Nick,

    Thanks for reporting this. I'll put in a ticket to have recallSpots.py refactored.

    --
    ~/Adam English

     

  • Adam English

    Adam English - 2015-03-26

    FYI - There is no longer a recallSpots.py procedure. Instead, you still call Honey.py spots with the added parameter of --hon

     

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