IndexError in __getitem__

[ruithe...@gmail.com]

Hello, i am getting the index error while trying to run an analysis.

Traceback (most recent call last):

  File "SDT_Linux64.py", line 158, in <module>

    dic_id_score[str(l1[i]) + "_" + str(l2[i])]=Get_Similarity(name_out,alg)

  File "SDT_Linux64.py", line 83, in Get_Similarity

    if recs[0].seq[i]!="-" and recs[1].seq[i]!="-":

  File "/home/user1/sdt/SDT_Linux64/Bio/Seq.py", line 211, in __getitem__

    return self._data[index]

IndexError: string index out of range

any idea what could generate this or how to solve? i even tried to give pre-aligned sequences, but the error persists. Somehow index is becoming higher than the length.

[Brejnev Muhire]

Hi, It seems the problem is in reading the sequences.

You could do two things:

1. Run the program using the give test.fas file and see if it works

2. If it works the problem could be the formatting to the sequence file.

3. Let me know how it goes, if need be you can send me the file causing the error for me to debug the code. my email: mubr...@gmail.com