mengyao
commented
1 year ago You can use -c option to get the full info.
Mengyao
On Jun 27, 2023, at 9:44 PM, SyedKumailHussainNaqvi @.***> wrote:
Hi @mengyao https://github.com/mengyao I am using the Python wrapper ssw_lib.py with this command python pyssw.py "/home/biolab/src/target_peptide.fasta" "/home/biolab/src/query_peptide.fasta" but I'm missing the begin of the alignments in the output.
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1acy_L query_name: 1acy_p optimal_alignment_score: 6 strand: + target_end: 76 query_end: 18
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1n0x_H query_name: 1acy_p optimal_alignment_score: 4 strand: + target_end: 26 query_end: 23
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1n0x_L query_name: 1acy_p optimal_alignment_score: 6 strand: + target_end: 75 query_end: 18
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1qgc_A query_name: 1acy_p optimal_alignment_score: 6 strand: + target_end: 124 query_end: 18
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1vrk_A query_name: 1acy_p optimal_alignment_score: 4 strand: + target_end: 5 query_end: 18
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1acy_L query_name: 1n0x_p optimal_alignment_score: 4 strand: + target_end: 25 query_end: 16
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1n0x_H query_name: 1n0x_p optimal_alignment_score: 4 strand: + target_end: 24 query_end: 16
fasta files.zip https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/files/11888654/fasta.files.zip — Reply to this email directly, view it on GitHub https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/issues/88, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEVK5FR4RNZ5ZI23Q47OXTXNOD7ZANCNFSM6AAAAAAZWLKAEA. You are receiving this because you were mentioned.
SyedKumailHussainNaqvi
Hi @mengyao I am using the Python wrapper ssw_lib.py with this command python pyssw.py "/home/biolab/src/target_peptide.fasta" "/home/biolab/src/query_peptide.fasta" but I'm missing the begin of the alignments in the output.
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1acy_L query_name: 1acy_p optimal_alignment_score: 6 strand: + target_end: 76 query_end: 18
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1n0x_H query_name: 1acy_p optimal_alignment_score: 4 strand: + target_end: 26 query_end: 23
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1n0x_L query_name: 1acy_p optimal_alignment_score: 6 strand: + target_end: 75 query_end: 18
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1qgc_A query_name: 1acy_p optimal_alignment_score: 6 strand: + target_end: 124 query_end: 18
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1vrk_A query_name: 1acy_p optimal_alignment_score: 4 strand: + target_end: 5 query_end: 18
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1acy_L query_name: 1n0x_p optimal_alignment_score: 4 strand: + target_end: 25 query_end: 16
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. target_name: 1n0x_H query_name: 1n0x_p optimal_alignment_score: 4 strand: + target_end: 24 query_end: 16
fasta files.zip