Skip to content

Feature request: Check for correct reference in input #4

Description

@mnshgl0110

I provided the following incorrect table as input:

chm13_mat.bam	chm13_matsyri.out
chm13_pat.bam	chm13_patsyri.out
mat_pat.bam	mat_patsyri.out

which resulted in the following error:

pansyn.find_multisyn(syns, alns, only_core=True)
Traceback (most recent call last):
  File "/srv/netscratch/dep_mercier/grp_schneeberger/software/anaconda3_2021/envs/mgpy3.8/lib/python3.8/site-packages/IPython/core/interactiveshell.py", line 3398, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-15-4c7dca4baca4>", line 1, in <cell line: 1>
    pansyn.find_multisyn(syns, alns, only_core=True)
  File "pansyri/pyxfiles/pansyn.pyx", line 262, in pansyri.pansyn.find_multisyn
  File "pansyri/pyxfiles/pansyn.pyx", line 132, in pansyri.pansyn.find_overlaps
  File "pansyri/pyxfiles/util.pyx", line 85, in pansyri.util.get_orgs_from_df
TypeError: reduce() of empty sequence with no initial value

Pansyri should check that the input table:

  1. Have same reference
  2. The files are indeed alignment and syri output files

If the input file is incorrect then it should throw an informative error.

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions