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get_RNA_seq_amount.py
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get_RNA_seq_amount.py
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__usage__ = """
python get_RNA_seq_amount.py
--cov_dir <FULL_PATH_TO_FOLDER_WITH_COVERAGE_FILES>
--out <FULL_PATH_TO_OUTPUT_FILE>
"""
import glob, os, sys
def main( arguments ):
"""! @brief get amount of RNA-Seq reads """
cov_file_dir = arguments[ arguments.index( '--cov_dir' ) +1 ]
output_file = arguments[ arguments.index( '--out' ) +1 ]
cov_files = glob.glob( cov_file_dir + "*.cov" )
print "number of detected cov files: " + str( len( cov_files ) )
with open( output_file, "a", 0 ) as out:
for filename in sorted( cov_files ):
total_cov = []
with open( filename, "r" ) as f:
line = f.readline()
while line:
parts = line.strip().split('\t')
total_cov.append( float( parts[-1] ) )
line = f.readline()
if len( total_cov ) == 1000000:
total_cov = [ sum( total_cov ) ]
out.write( filename.split('/')[-1].split('.')[0] + '\t' + str( sum( total_cov ) ) + '\n' )
if __name__ == '__main__':
if '--cov_dir' in sys.argv and '--out' in sys.argv:
main( sys.argv )
else:
sys.exit( __usage__ )