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Fix bug on the graph construction. Set -m to 8
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@iprada
iprada committed Nov 12, 2019
1 parent e7f1bf2 commit 13a3478
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Showing 3 changed files with 25 additions and 16 deletions.
8 changes: 4 additions & 4 deletions circlemap/circle_map.py
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Original file line number Diff line number Diff line change
Expand Up @@ -391,8 +391,8 @@ def args_realigner(self):
default=0.99)

alignment_options.add_argument('-m', '--min_sc', type=float, metavar='',
help="Minimum soft-clipped length to attempt the realignment. Default: 5",
default=5)
help="Minimum soft-clipped length to attempt the realignment. Default: 8",
default=8)

alignment_options.add_argument('-g', '--gap_open', type=int, metavar='',
help="Gap open penalty in the position specific scoring matrix. Default: 5",
Expand Down Expand Up @@ -510,8 +510,8 @@ def args_realigner(self):
default=0.99)

alignment_options.add_argument('-m', '--min_sc', type=float, metavar='',
help="Minimum soft-clipped length to attempt the realignment. Default: 5",
default=5)
help="Minimum soft-clipped length to attempt the realignment. Default: 8",
default=8)

alignment_options.add_argument('-g', '--gap_open', type=int, metavar='',
help="Gap open penalty in the position specific scoring matrix. Default: 5",
Expand Down
2 changes: 2 additions & 0 deletions circlemap/realigner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -190,11 +190,13 @@ def realign(self,peaks):




if len(candidate_mates) > 0:


realignment_interval_extended = get_realignment_intervals(candidate_mates,extension,self.interval_p,
self.verbose)


if realignment_interval_extended is None:
continue
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31 changes: 19 additions & 12 deletions circlemap/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -579,6 +579,9 @@ def insert_size_dist(sample_size,mapq_cutoff,qname_bam):
std = np.std(insert_length)
return(mean, std)

def normalize_probability_matrix(pandas_df):
return(pandas_df)

def get_realignment_intervals(bed_prior,interval_extension,interval_p_cutoff,verbose):


Expand Down Expand Up @@ -614,6 +617,7 @@ def get_realignment_intervals(bed_prior,interval_extension,interval_p_cutoff,ver
candidate_mates = candidate_mates_dataframe.groupby((candidate_mates_dataframe.end.shift()-candidate_mates_dataframe.start).lt(0).cumsum()).agg({'chrom':'first','start':'first','end':'last','probability':'sum'})

sum = np.sum(float(x[3]) for index, x in candidate_mates.iterrows())
candidate_mates['probability'] = candidate_mates['probability'] / sum


elif np.any(read_types == 'SC') == True and (np.any(read_types == 'DR') == True or np.any(read_types == 'SA') == True):
Expand All @@ -628,6 +632,7 @@ def get_realignment_intervals(bed_prior,interval_extension,interval_p_cutoff,ver


sum = np.sum(float(x[3]) for index,x in candidate_mates.iterrows())
candidate_mates['probability'] = candidate_mates['probability']/sum



Expand All @@ -639,6 +644,8 @@ def get_realignment_intervals(bed_prior,interval_extension,interval_p_cutoff,ver
extended = []




#if argmax is turn on interval_p is 0
if interval_p_cutoff == 0:
#argmax(probability)
Expand All @@ -654,28 +661,28 @@ def get_realignment_intervals(bed_prior,interval_extension,interval_p_cutoff,ver
end = row['end'] + interval_extension

if start < 0:
extended.append([row['chrom'], str(0), int(round(end))])
extended.append([row['chrom'], str(0), int(round(end)),float(row['probability'])])

else:
extended.append([row['chrom'], int(round(start)), int(round(end))])
extended.append([row['chrom'], int(round(start)), int(round(end)),float(row['probability'])])

elif 'L' in orientation:

start = row['start'] - interval_extension

if start < 0:
extended.append([row['chrom'], str(0), row['end']])
extended.append([row['chrom'], str(0), row['end'],float(row['probability'])])

else:
extended.append([row['chrom'], int(round(start)), row['end']])
extended.append([row['chrom'], int(round(start)), row['end'],float(row['probability'])])

elif 'R' in orientation:

end = row['end'] + interval_extension

extended.append([row['chrom'], row['start'], int(round(end))])
extended.append([row['chrom'], row['start'], int(round(end)),float(row['probability'])])

return (pd.DataFrame.from_records(extended, columns=['chrom', 'start', 'end']))
return (pd.DataFrame.from_records(extended, columns=['chrom', 'start', 'end','probability']))

else:

Expand All @@ -693,29 +700,29 @@ def get_realignment_intervals(bed_prior,interval_extension,interval_p_cutoff,ver
end = interval['end'] + interval_extension

if start < 0:
extended.append([interval['chrom'], str(0), int(round(end))])
extended.append([interval['chrom'], str(0), int(round(end)),float(interval['probability'])])

else:
extended.append([interval['chrom'], int(round(start)), int(round(end))])
extended.append([interval['chrom'], int(round(start)), int(round(end)),float(interval['probability'])])

elif 'L' in orientation:

start = interval['start'] - interval_extension

if start < 0:
extended.append([interval['chrom'], str(0), interval['end']])
extended.append([interval['chrom'], str(0), interval['end'],float(interval['probability'])])

else:
extended.append([interval['chrom'], int(round(start)), interval['end']])
extended.append([interval['chrom'], int(round(start)), interval['end'],float(interval['probability'])])

elif 'R' in orientation:

end = interval['end'] + interval_extension

extended.append([interval['chrom'], interval['start'], int(round(end))])
extended.append([interval['chrom'], interval['start'], int(round(end)),float(interval['probability'])])


return(pd.DataFrame.from_records(extended,columns=['chrom','start','end']))
return(pd.DataFrame.from_records(extended,columns=['chrom','start','end','probability']).sort_values(by=['probability'],ascending=[False]))


except BaseException as e:
Expand Down

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