chrisgulvik/c-sstar

CLI Sequence Search Tool for Antimicrobial Resistance

c-sstar's Issues

Feature Request: denote whether hit is on edge of contig or not

Denoting gene location with respect to the contig would be helpful in assessing confidence of an incomplete match.

contig_A |====================|
match.........................'-->'

versus

contig_B |====================|
match...........................................'-->'

Bitscore int comparison error

Halts on error due to integer comparison of bitscore, which occasionally can be a non-int.

For example:

Traceback (most recent call last):
  File "/scicomp/home/kqj9/c-SSTAR/c-SSTAR", line 132, in <module>
    main()
  File "/scicomp/home/kqj9/c-SSTAR/c-SSTAR", line 118, in main
    if int(best[6]) < int(candidate[6]):
ValueError: invalid literal for int() with base 10: '64.4' 

problem relying on CD-HIT group values for assignments

@alawsin found blaSHV occur in >1 CD-HIT group in the ARG-ANNOT database. Because the group numbers are >1 apart, both are reported yet just one of the two should be reported. This is an example blast output where just one should be selected as best hit:

245__blaSHV__blaSHV-11_2_HM751098__00748 2013732592_S5_L001_Assembled_77 100 861 0 0 1 861 4361 5221 0 1553 861 ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA

207__blaSHV__blaSHV-100_1_AM941846__01138 2013732592_S5_L001_Assembled_77 95.11 900 5 39 1 900 4361 5221 0 1456 900 ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAAC---------------------------------------AAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA