34 lines
865 B
Python
Executable file
34 lines
865 B
Python
Executable file
#!/usr/bin/env python3
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from Bio import SeqIO
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from Bio import pairwise2
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from Bio.pairwise2 import format_alignment
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from align import myalign
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import re
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import os
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os.chdir('/home/tanu/git/LSHTM_analysis/scripts/examples')
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def main():
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"""
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align ref_seq and pdb_seq
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# FIXME: pass command line args i.e filename
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"""
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my_dict = {}
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align_fastas_to_align = open('align_fastas.txt', 'r')
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for record in SeqIO.parse(align_fastas_to_align,"fasta"):
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myid = record.id
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seq = str(record.seq)
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my_dict.update({myid : seq})
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my_keys = list(my_dict.keys())
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my_ref_seq = my_dict[my_keys[0]]
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my_pdb_seq = my_dict[my_keys[1]]
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fasta_alignment = myalign(my_ref_seq, my_pdb_seq)
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print(fasta_alignment)
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print('class:', type(fasta_alignment))
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if __name__ == '__main__':
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main()
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