python

[leonvgurp]

Hi all,

I'm trying to run sinto on our local cluster. We have sinto v0.7.3.1 available with python 3.8.6. GCC v10.2.0 and OpenMPI v4.0.5 are loaded in the background. I use the following code to generate my fragments file:

sinto fragments -p 8 \
      -b /dir/file.bam \
      -f /dir/file.bed \
      --barcode_regex "[^:]*" \
      --use_chrom "*"

This generates the following output (with errors):

Function run_fragments called with the following arguments:

bam   /dir/file.bam
fragments   /dir/file.bed
min_mapq    30
nproc 8
barcodetag  CB
cells None
barcode_regex     [^:]*
use_chrom   *
max_distance      5000
min_distance      10
chunksize   500000
func  <function run_fragments at 0x2b3f2e8843a0>
Traceback (most recent call last):
  File "/opt/ebsofts/sinto/0.7.3.1-foss-2020b-Python-3.8.6/bin/sinto", line 8, in <module>
    sys.exit(main())
  File "/opt/ebsofts/sinto/0.7.3.1-foss-2020b-Python-3.8.6/lib/python3.8/site-packages/sinto/arguments.py", line 346, in main
    options.func(options)
  File "/opt/ebsofts/sinto/0.7.3.1-foss-2020b-Python-3.8.6/lib/python3.8/site-packages/sinto/utils.py", line 21, in wrapper
    func(args)
  File "/opt/ebsofts/sinto/0.7.3.1-foss-2020b-Python-3.8.6/lib/python3.8/site-packages/sinto/cli.py", line 45, in run_fragments
    fragments.fragments(
  File "/opt/ebsofts/sinto/0.7.3.1-foss-2020b-Python-3.8.6/lib/python3.8/site-packages/sinto/fragments.py", line 470, in fragments
    chrom = utils.get_chromosomes(bam, keep_contigs=chromosomes)
  File "/opt/ebsofts/sinto/0.7.3.1-foss-2020b-Python-3.8.6/lib/python3.8/site-packages/sinto/utils.py", line 134, in get_chromosomes
    pattern = re.compile(keep_contigs)
  File "/opt/ebsofts/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/re.py", line 252, in compile
    return _compile(pattern, flags)
  File "/opt/ebsofts/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/re.py", line 304, in _compile
    p = sre_compile.compile(pattern, flags)
  File "/opt/ebsofts/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/sre_compile.py", line 764, in compile
    p = sre_parse.parse(p, flags)
  File "/opt/ebsofts/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/sre_parse.py", line 948, in parse
    p = _parse_sub(source, state, flags & SRE_FLAG_VERBOSE, 0)
  File "/opt/ebsofts/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/sre_parse.py", line 443, in _parse_sub
    itemsappend(_parse(source, state, verbose, nested + 1,
  File "/opt/ebsofts/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/sre_parse.py", line 668, in _parse
    raise source.error("nothing to repeat",
re.error: nothing to repeat at position 0
srun: error: node245: task 0: Exited with exit code 1

We suspect this may be caused by the python version, but not sure. Could there be another reason why these errors are produced?

[timoast]

I think you just need to set --use_chrom "." rather than "*". If you run this:

import re
re.compile("*")

you should see a similar error

[leonvgurp]

This makes me feel very silly, but it indeed solves my problem. Thanks!

As a follow-up on this question, if I may. I'm not sure completely about the syntax to select the barcode regex. If I would, for example, want to use the 2nd column between colons instead of the first, what would be the instruction for that instead of "[^:]*"

Is this purely sed-based?

[timoast]

The string provided will be a regular expression used to detect the barcode. It's useful to test out a regular expression using https://regex101.com/ to find the expression that works for your format.