nkrumm / conifer Goto Github PK

Yes.

@nkrumm
conifer throws out this error please do mention what i did wrong
have attached the probes.txt file and the indexed bam file that i am using
probes.txt

   [INIT] Successfully read in 194080 probes from ../sampledata/probes.txt
   [RUNNING] Counting total number of reads in bam file...
   [RUNNING] Found 2083467 reads
   [RUNNING] Calculating RPKM values...
   conifer.py:617: RuntimeWarning: invalid value encountered in divide
      rpkm = (10**9*(readcount)/(exon_bp))/(total_reads)

when i tried conifer on another machine this error pops up

Traceback (most recent call last): File "conifer.py", line 682, in <module> args.func(args) File "conifer.py", line 564, in CF_bam2RPKM if not f._hasIndex(): AttributeError: 'pysam.csamfile.Samfile' object has no attribute '_hasIndex'

your help is much appreciated

https://github.com/nkrumm/CoNIFER/blob/master/conifer.py#L220-L224

the count variable does not change, resulting in np.stdev being called on last chromosome only!

When a user plots many calls in one command using the
python conifer.py plotcalls --input analysis.hdf5 --calls calls.txt --outputdir call_imgs
command, matplotlib does not correctly close all the figures and eventually chokes.

Dear Nik,

I am trying to use CoNIFER but I have the following bug when running conifer.py:
Traceback (most recent call last):
File "conifer.py", line 682, in
args.func(args)
File "conifer.py", line 545, in CF_bam2RPKM
probes = cf.loadProbeList(probe_fn)
File "conifer_functions.py", line 96, in loadProbeList
probes.append({'probeID': probeID, 'chr':chrStr2Int(row['chr']),'start':int(row['start']),'stop':int(row['stop']), 'name':row['name']})
KeyError: 'stop'

Line 112 in conifer_functions.py should be:
return np.loadtxt(rpkm_filename, dtype=np.float, delimiter="\t", skiprows=0, usecols=[2])
instead of
return np.loadtxt(samples[s], dtype=np.float, delimiter="\t", skiprows=0, usecols=[2])