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Fix fetch_reads #493

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Fix fetch_reads #493

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2891801
Fix fetch_reads
Nov 20, 2016
9b826d6
Avoid problem in unzip
Dec 13, 2016
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8 changes: 4 additions & 4 deletions falcon_kit/mains/fetch_reads.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,10 +64,10 @@ def pid_to_oid(pid):
with open(map_fn, 'r') as f:
for row in f:
row = row.strip().split()
hit_ctg = row[1]
hit_ctg = hit_ctg.split('-')[0]
if hit_ctg not in read_set and int(row[3]) == 0:
o_id = pid_to_oid(row[0])
o_id = pid_to_oid(row[0])
if o_id not in read_set and int(row[3]) == 0:
hit_ctg = row[1]
hit_ctg = hit_ctg.split("-")[0]
read_set[o_id] = hit_ctg
ctg_id_hits[hit_ctg] = ctg_id_hits.get(hit_ctg, 0) + 1

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10 changes: 5 additions & 5 deletions falcon_kit/mains/graph_to_contig.py
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Expand Up @@ -258,11 +258,11 @@ def main(argv=None):
delta_len = len(seq) - len(base_seq)
idt = 0.0
cov = 0.0
if len(base_seq) > 2000 and len(seq) > 2000:
aln_data, x, y = get_aln_data(base_seq, seq)
if len( aln_data ) != 0:
idt = 1.0-1.0*aln_data[-1][-1] / aln_data[-1][-2]
cov = 1.0*(aln_data[-1][3]-aln_data[-1][2])/aln_data[-1][4]
#if len(base_seq) > 2000 and len(seq) > 2000:
# aln_data, x, y = get_aln_data(base_seq, seq)
# if len( aln_data ) != 0:
# idt = 1.0-1.0*aln_data[-1][-1] / aln_data[-1][-2]
# cov = 1.0*(aln_data[-1][3]-aln_data[-1][2])/aln_data[-1][4]

atig_output.append( (v, w, atig_path, total_length, total_score, seq, atig_path_edges, delta_len, idt, cov) )

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