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Fix qual_vs_pos #145

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Fix qual_vs_pos #145

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070141f
add sys import
shiltemann Jul 9, 2017
727d74a
replace jpg with png
shiltemann Jul 9, 2017
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11 changes: 5 additions & 6 deletions poretools/qual_v_pos.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
from collections import defaultdict
import pandas
import matplotlib.pyplot as plt
import sys

#logging
import logging
Expand All @@ -12,7 +13,7 @@ def run(parser, args):
""" returns boxplot with qual scores for each bin/position"""
qualpos = defaultdict(list)
bin_width = args.bin_width

for fast5 in Fast5File.Fast5FileSet(args.files):
if args.start_time or args.end_time:
read_start_time = fast5.get_start_time()
Expand All @@ -32,7 +33,7 @@ def run(parser, args):
continue

for fq in fqs:
if fq is None or len(fq.seq) < args.min_length or len(fq.seq) > args.max_length:
if fq is None or len(fq.seq) < args.min_length or len(fq.seq) > args.max_length:
continue

ctr = 0
Expand All @@ -53,14 +54,12 @@ def run(parser, args):
if args.saveas is not None:
logger.info("Writing plot to file...")
plot_file = args.saveas
if plot_file.endswith(".pdf") or plot_file.endswith(".jpg"):
if plot_file.endswith(".pdf") or plot_file.endswith(".png"):
plt.savefig(plot_file)
else:
logger.error("Unrecognized extension for %s! Try .pdf or .jpg" % (plot_file))
logger.error("Unrecognized extension for %s! Try .pdf or .png" % (plot_file))
sys.exit()

else:
logger.info("Showing plot...")
plt.show()