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Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
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I have a problem when I used recycler #5

Closed OAF12 closed 7 years ago

OAF12 commented 7 years ago

This was the commad: python recycle.py -g assembly_graph.fastg -k 55 -b reads_pe_primary.sort.bam but I got the below error ================== path, coverage levels when added ==================== Traceback (most recent call last): File "recycle.py", line 131, in last_node_count = len(COMP.nodes()) TypeError: object of type 'generator' has no len() what should be done to solve this problem? Thanks

rozovr commented 7 years ago

Hi @OAF12 ,

I apologize for taking very long to reply. Did you manage to resolve this issue? If not, can you help me replicate it?

Thanks, R

OAF12 commented 7 years ago

?Hi,

I didnt manage to solve the problem till now. How you can help me to solve it?

Best regards

Omneya

From: Roye Rozov notifications@github.com Sent: Saturday, February 25, 2017 22:57 To: Shamir-Lab/Recycler Cc: Omneya Ahmed Abdel Hafez Sayed Osman; Mention Subject: Re: [Shamir-Lab/Recycler] I have a problem when I used recycler (#5)

Hi @OAF12https://github.com/OAF12 ,

I apologize for taking very long to reply. Did you manage to resolve this issue? If not, can you help me replicate it?

Thanks, R

- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Shamir-Lab/Recycler/issues/5#issuecomment-282515416, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AXrXpnVnqWZ2o97S0oVf0zD_eYnAShY4ks5rgKO7gaJpZM4LXnxS.

rozovr commented 7 years ago

Omneya,

Since I haven't seen this pop up before, I would suggest first ruling out installation issues. Can you please try to reinstall using bioconda? That should make sure all the dependencies are in place.

Thanks, R