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mengyao / Complete-Striped-Smith-Waterman-Library

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not seeing target_begin in blast output in python #56

Closed juancresc closed 2 years ago

juancresc commented 6 years ago

I'm missing the begin of the alignments in the output

` python pyssw.py ../../../miteParser/demo2.fa ../../../miteParser/demo2.fa target_name: 1 query_name: 1 optimal_alignment_score: 2398 suboptimal_alignment_score: 1196 strand: + target_end: 1200 query_end: 1200

target_name: 1 query_name: 1 optimal_alignment_score: 2398 suboptimal_alignment_score: 1196 strand: + target_end: 1200 query_end: 1200

target_name: 2 query_name: 1 optimal_alignment_score: 124 suboptimal_alignment_score: 56 strand: + target_end: 1148 query_end: 569

target_name: 1 query_name: 1 optimal_alignment_score: 2398 suboptimal_alignment_score: 1196 strand: + target_end: 1200 query_end: 1200

target_name: 1 query_name: 1 optimal_alignment_score: 2398 suboptimal_alignment_score: 1196 strand: + target_end: 1200 query_end: 1200

target_name: 2 query_name: 1 optimal_alignment_score: 124 suboptimal_alignment_score: 56 strand: + target_end: 1148 query_end: 569

target_name: 1 query_name: 2 optimal_alignment_score: 124 suboptimal_alignment_score: 48 strand: + target_end: 569 query_end: 1148

target_name: 1 query_name: 2 optimal_alignment_score: 124 suboptimal_alignment_score: 48 strand: + target_end: 569 query_end: 1148

target_name: 2 query_name: 2 optimal_alignment_score: 2376 suboptimal_alignment_score: 1188 strand: + target_end: 1189 query_end: 1189

CPU time: 0.0409369468689 seconds`