`split_fastx` on fastq files

[chAwater]

A Minimal Working Example:

• inputs.fq

  
  @test1
  AAAAATTTTT

• aaaaaaaaaa

• command

  split_fastx inputs.fq outputs.fq 5

• outputs.fq

  
  @test1_chunk0 chunk_length=5
  <itertools.chain object at 0x7febfb44ba90>

• <itertools.chain object at 0x7febfb44bb38> @test1_chunk1 chunk_length=5 <itertools.chain object at 0x7febfb44bba8>

• <itertools.chain object at 0x7febfb44bbe0> @test1_chunk2 chunk_length=5 <itertools.chain object at 0x7febfb44bc50>

• <itertools.chain object at 0x7febfb44ba58> @test1_chunk3 chunk_length=5 <itertools.chain object at 0x7febfb44b940>

• <itertools.chain object at 0x7febfb44bb70> @test1_chunk4 chunk_length=5 <itertools.chain object at 0x7febfb44bb00>

• <itertools.chain object at 0x7febfb44bc18> @test1_chunk5 chunk_length=5 <itertools.chain object at 0x7febfb44bba8>

• <itertools.chain object at 0x7febfb44bbe0> @test1_chunk6 chunk_length=5 <itertools.chain object at 0x7febfb44ba90>

• <itertools.chain object at 0x7febfb44bb38> @test1_chunk7 chunk_length=5 <itertools.chain object at 0x7febfb44b940>

• <itertools.chain object at 0x7febfb44bb70> @test1_chunk8 chunk_length=5 <itertools.chain object at 0x7febfb44bc50>

• <itertools.chain object at 0x7febfb44ba58> @test1_chunk9 chunk_length=5 <itertools.chain object at 0x7febfb44bba8>

• <itertools.chain object at 0x7febfb44bbe0>

---

• This works fine if change fastq to fasta

  head -n2 inputs.fq | split_fastx - /dev/stdout 5

• output

  >test1_chunk0 chunk_length=5
  AAAAA
  >test1_chunk1 chunk_length=5
  TTTTT

---

I think the problem is on https://github.com/nanoporetech/pomoxis/blob/ad462b00de316f5ef0825ccbac0dc45bb85d9989/pomoxis/util.py#L105

that zip two itertools.chain objects.

[ftostevin-ont]

Thanks for the report. This should be fixed in v0.3.9

[chAwater]

Thanks!

ref: https://github.com/nanoporetech/pomoxis/commit/e23019fc7de9570e83daf74d3f0e14bfc80ceb5e