Commit 421d784b authored by Mathieu Giraud's avatar Mathieu Giraud option -a, display only tagged clones in the .analysis file

TODO: The path to the .analysis file should not be hard-coded.
parent 9e919592
......@@ -3,6 +3,7 @@
from __future__ import print_function
import fuse
import analysis
import sys
import argparse
import re
......@@ -11,6 +12,7 @@ parser = argparse.ArgumentParser(description = 'Output a LaTeX table for clones
parser.add_argument('--min-ratio', '-r', type=float, default=.01, help='minimal reads ratio of the clone (%(default).3f)')
parser.add_argument('--min', '-m', type=int, default=1, help='minimal number of reads in the clone (%(default)d)')
parser.add_argument('--top', '-t', type=int, default=5, help='maximal number of clones to displlay (%(default)d)')
parser.add_argument('--analysis', '-a', action='store_true', help='filter clones tagged in the relevant .analysis file (experimental, hardcoded)')
parser.add_argument('--verbose', '-v', action='store_true', help='verbose output')
parser.add_argument('file', nargs='+', help='''.vidjil files''')
......@@ -31,12 +33,27 @@ def main():
m = regex_filename.match(i)
i_short = if m else i
if args.analysis:
# TODO: hardcoded for output of
# should be more flexible
ii = 'data.vidjil/' + 'pat-' + i_short +'.analysis'
data_analysis = analysis.Analysis()
data_analysis = None
print('%s %% %s' % (i_short, i))
print('%% ', data.d["reads"])
segmented_reads = data.d['reads'].d['segmented'][0]
out = []
for w in data:
if data_analysis:
tag = data_analysis.tag_of_clone(w)
if not tag:
tag = ''
reads = w.d['reads'][0]
ratio = float(reads)/segmented_reads
if reads >= args.min and ratio >= args.min_ratio:
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