file format wrong about cdna_cupcake

[hmyh1202]

Recentlly I have got the same problem, hard to read the fusion_finder.py

[Magdoll]

Hi,

Please give me the full set of commands you are running.

[hmyh1202]

My code is：
python fusion_finder.py
--input sample.hq.fastq
--fq
--sam gmap.sort.sam
--prefix sample
--min_locus_coverage 0.1
--min_total_coverage 0.99
--min_dist_between_loci 100000
--cluster_report_csv report.csv

It should be related to sam file format. When I run alignment using GMAP I did not use "-n 0 -z sense_force ". Now is OK.

[Magdoll]

OK thanks.

[hmyh1202]

Traceback (most recent call last):
File "Python-2.7.8/bin/fusion_finder.py", line 393, in
min_dist_between_loci=args.min_dist_between_loci)
File "Python-2.7.8/bin/fusion_finder.py", line 301, in fusion_main
o = merge_fusion_exons(v, max_fusion_point_dist=100, max_exon_end_dist=0, allow_extra_5_exons=allow_extra_5_exons)
File "fusion_finder.py", line 207, in merge_fusion_exons
if all(is_fusion_compatible(r1, r2, max_fusion_point_dist, max_exon_end_dist, allow_extra_5_exons) for r2 in r2s):
File "fusion_finder.py", line 207, in
if all(is_fusion_compatible(r1, r2, max_fusion_point_dist, max_exon_end_dist, allow_extra_5_exons) for r2 in r2s):
File "Python-2.7.8/bin/fusion_finder.py", line 153, in is_fusion_compatible
type = compare_junctions(r1, r2)
File:/Python-2.7.8/lib/python2.7/site-packages/cupcake/tofu/compare_junctions.py", line 21, in compare_junctions
strand = r1.strand
AttributeError: GMAPSAMRecord instance has no attribute 'strand'

[hmyh1202]

Alignment para
bin/gmap -D /home/share/gmap_db/ -d hg38 -f samse -n 0 -t 12 -z sense_force hq_isoforms.fastq

[hmyh1202]

May be the issue of 'strand = r1.strand' in compare_junctions.py

strand = r1.flag.strand

[Magdoll]

Hi,
I have fixed this issue. Please update to the latest commit in Cupcake (version 3.6, commit 9848e783978cc48e39d8f5220ef824c86c8df874).

You can verify that you have the same commit in your repo by

$ git rev-parse HEAD
9848e783978cc48e39d8f5220ef824c86c8df874

Let me know if this fixes the problem.
Thanks!
--Liz