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Edit and run



In [1]:

    
from DNASkittleUtils.Contigs import read_contigs, Contig, write_contigs_to_file



In [2]:

    
contigs = read_contigs("D:\Genomes\Ash BATG-0.5-CLCbioSSPACE\BATG-0.5-CLCbioSSPACE.fa")

Using the two contig names you sent me it's simplest to do this:



In [5]:

    
desired_contigs = ['Contig' + str(x) for x in [1131, 3182, 39106, 110, 5958]]
desired_contigs









    Out[5]:





['Contig1131', 'Contig3182', 'Contig39106', 'Contig110', 'Contig5958']

If you have a genuinely big file then I would do the following:

desired_contigs = open('Data/BATG-selects.txt', 'r').read().splitlines() unique_desired = set(desired_contigs) len(unique_desired), desired_contigs[:10]



In [7]:

    
grab = [c for c in contigs if c.name in desired_contigs]
len(grab)









    Out[7]:





5

Ya! There's two contigs.

assert len(grab) == len(unique_desired)



In [8]:

    
import os
print(os.getcwd())
write_contigs_to_file('data2/sequences_desired.fa', grab)









    



D:\josiah\Documents\Research\Barcoding-Fraxinus
Done writing  5 contigs and 682,487bp



In [9]:

    
[c.name for c in grab[:100]]









    Out[9]:





['Contig110', 'Contig1131', 'Contig3182', 'Contig5958', 'Contig39106']



In [1]:

    
import os
os.path.realpath('')









    Out[1]:





'D:\\josiah\\Documents\\Research\\Barcoding-Fraxinus'



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