merge_bed.py chokes on find_circ2 output

[mschilli87]

Trying to combine two runs analyzed with the latest find_circ2 by

merge_bed.py \
  --format=2 \
  <(zcat sample1.circ_splice_sites.bed.gz) \
  <(zcat sample2.circ_splice_sites.bed.gz) \
| pigz \
  --best \
> merged.circ_splice_sites.bed.gz

I get

circ_splice_sites
Traceback (most recent call last):
  File "merge_bed.py", line 176, in <module>
    cols = [comstr] + consensus_cols(lines,comb)
  File "merge_bed.py", line 138, in consensus_cols
    parts.append(str(col_map[i](column)))
  File "merge_bed.py", line 123, in <lambda>
    9 : lambda values : array(values,dtype=int).sum(), # sum ov_linear_A
ValueError: invalid literal for long() with base 10: '0.5'

@marvin-jens: I'm willing to fix it myself but I'll need some directions. ;)

[mschilli87]

@retaj: Maybe you can comment how you do these kind of things? ciRcus/BED6 only/Not at all?

[marvin-jens]

Hi Marcel, didn't see the notification as MDC email is checked only intermittently. I'd prefer if you guys would move this functionality to ciRcus. Table merging is definitely sth that's handled more cleanly in R. The merge_bed.py is a bit hacky, to say the least, and I wouldn't be sad to see it go away. Thanks for inquiring.

[mschilli87]

Allright, marked as [wontfix].

Reading find_circ2 output is supported in ciRcus since about a week (BIMSBbioinfo/ciRcus@c8ef7f5).

I'll leave this issue open until we have

• implemented proper flag merging in ciRcus,
• updated the find_circ2 README accordingly &
• deleted merge_bed.py from this repository.

PS: It is possible to update your email on github. ;)
PPS: Make sure to keep the old one (as non-primary) to not loose association of old commits to you profile.

[marvin-jens]

Thanks Marcel. I already changed email settings yesterday, exactly as you propose.

…

On Tuesday, February 14, 2017 11:29:15 PM EST Marcel Schilling wrote: Allright, marked as [wontfix]. Reading `find_circ2` output is supported in [`ciRcus](https:/BIMSBbioinfo/ciRcus) since about a week (BIMSBbioinfo/ciRcus@c8ef7f55d1c2003b9d9c7691c954 2af999ecb2b7). I'll leave this issue open until we have - [ ] implemented proper flag merging in `ciRcus` & - [ ] updated the `find_circ2` `README` accordingly. PS: It is possible to [update your email on github](https://help.github.com/articles/changing-your-primary-email-addres s/). ;) PPS: Make sure to keep the old one (as non-primary) to not loose association of old commits to you profile.