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import matplotlib.pyplot as plt
import sys
def get_nb_allele_distribution(gfa_file_name):
gfa_file=open(gfa_file_name)
sizes = []
for line in gfa_file:
if line[0]=='S':#S 2 34156l;-11363l;13698l;-26143h;10014l; RC:i:144
l=len(line.split()[2].split(';')[:-1])
sizes.append(l)
gfa_file.close()
return sizes
def get_sequence_size_distribution(gfa_file_name):
gfa_file=open(gfa_file_name)
sizes = []
for line in gfa_file:
if line[0]=='S':#S 0 actgcaACAGCTGTTGAAAAGCCGGAATGTACTCTTCATTGCAAACATTTCAGGGATGAAGTGAAGAtgaattgCGACGTAGTATCCACACCAAGCCGGCGTTATCCGGTGAGGCGCAATGTTGCGGGGGCttt RC:i:11
sizes.append(len(line.split()[2]))
gfa_file.close()
return sizes
def plot_violin(sequence_sizes, nb_alleles, read_set_id):
fig, axes = plt.subplots(nrows=1, ncols=2, figsize=(10, 10))
axes[0].violinplot(sequence_sizes)
axes[0].set_title('Sequence size distribution')
axes[1].violinplot(nb_alleles)
axes[1].set_title('Nb alleles per sequence')
plt.savefig('distributions_'+read_set_id+'.png')
def main():
'''
Stats from a gfa file
'''
sequence_sizes=get_sequence_size_distribution(sys.argv[2]) #for each snp id: sequences[snp_id]=[left_unitig_len, right_unitig_len, upperseq, lowerseq]
nb_alleles=get_nb_allele_distribution(sys.argv[1])
plot_violin(sequence_sizes, nb_alleles, sys.argv[3])
if __name__ == "__main__":
main()
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