Hi,

Running MIRA for a contig threshold here. I am trying to plot the contig length and the number of iterations, but somehow, the plotter stops the program after a iteration. Any idea why?

import os
import sys
import shutil
import subprocess
import matplotlib.pyplot as plt
import numpy as np

name = sys.argv[1] + '-0'
ref_loc = sys.argv[2]
read_loc = sys.argv[3]

manifest = open('manifest-0.conf', 'w')
manifest.write('project = ' + name + '\njob = genome,mapping,accurate\nparameters = -GE:not=6 -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no COMMON_SETTINGS -SB:tor=no\nreadgroup\nis_reference\ndata = ' + ref_loc + '\nstrain = ' + name + '\nreadgroup = reads\ndata = ' + read_loc + '\ntechnology=solexa')
manifest.close()

avg_cov = 0
count = 0
new_avg_cov = 0
contig_length = 0

while new_avg_cov <= avg_cov * 2 or avg_cov == 0: #set threshold for average coverage points

    command1 = 'mira manifest-' + str(count) + '.conf'
    print(command1)

    avg_cov = new_avg_cov

    subprocess.call(command1, shell=True)

    print('MIRA is really done!')

    with open(name + '_assembly/' + name +'_d_info/'+ name +'_info_contigstats.txt') as f:
        print('Fishing for coverage:')
        for line in f:
            if not line.startswith('#'):
                new_avg_cov = float(line.split('\t')[5])


    with open(name + '_assembly/' + name +'_d_info/'+ name +'_info_contigstats.txt') as f:
        if not line.startswith('#'):
            contig_length = int(line.split('\t')[1])

    plt.scatter(count, contig_length)
    plt.xlabel("Number of iterations", fontsize=14)
    plt.ylabel("Length of assembled contig", fontsize=14)
    plt.axis([0,100, 0,200000])
    plt.pause(0.001)
    plt.show()

    new_bait = name + '_assembly/' + name +'_d_results/'+ name +'_out_AllStrains.unpadded.fasta'
    print('new bait is ' + new_bait)
    count += 1

    name = name.split('-')[0] + '-' + str(count)
    manifest = open('manifest-' + str(count) +'.conf', 'w')
    print('new manifest is ' + 'manifest-' + str(count) +'.conf')
    manifest.write('project = ' + name +'\njob = genome,mapping,accurate\nparameters = -GE:not=6 -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no COMMON_SETTINGS -SB:tor=no\nreadgroup\nis_reference\ndata = /home/radu/Desktop/new_test' + new_bait + '\nstrain = ' + name + '\nreadgroup = reads\ndata = ' + read_loc + '\ntechnology=solexa')
    manifest.close()

    if os.path.exists('./manifest-' + str(count-2) + '.conf'):
        os.remove('./manifest-' + str(count-2) + '.conf')
        shutil.rmtree('./' + name.split('-')[0] + '-' + str(count-2) + '_assembly/' )

Tried to use a line instead of a scatterplot, same result. I think It might be a problem with the manifest file, but i cant figure it out.