First version of the explore command

[alneberg]

TODO:

• Verify that this implementation works as intended
• Verify that the regular anglerfish demux is not tampered with
• Perhaps clean up the two different dockerfiles?

This buils on top of #58 so if that one is merged, the diff will be slightly smaller.

[alneberg]

Example output for a real dataset. Can of course be improved upon but it seems to work at least.

$ python anglerfish/explore/cli.py --fastq ../../minimap_all/APS770/reads.fastq.gz -o test_out_APS770 -t 10
INFO:explore:Running anglerfish explore
INFO:explore:Run uuid 4147c08d-c262-4bf6-9267-be00dca76ff5
INFO:explore:Aligning illumina_ud
INFO:explore:Aligning truseq
INFO:explore:Aligning truseq_dual
INFO:explore:Aligning nextera_legacy
INFO:explore:Aligning nextera_dual
INFO:explore:Parsing illumina_ud
INFO:explore:illumina_ud:i5 had 113979 good hits.
INFO:explore:illumina_ud:i7 had 203160 good hits.
INFO:explore:Adaptor illumina_ud is included in the analysis
INFO:explore:Parsing truseq
INFO:explore:truseq:i5 had 0 good hits.
INFO:explore:truseq:i7 had 5 good hits.
INFO:explore:Adaptor truseq is excluded from the analysis
INFO:explore:Parsing truseq_dual
INFO:explore:truseq_dual:i5 had 1 good hits.
INFO:explore:truseq_dual:i7 had 5 good hits.
INFO:explore:Adaptor truseq_dual is excluded from the analysis
INFO:explore:Parsing nextera_legacy
INFO:explore:nextera_legacy:i5 had 0 good hits.
INFO:explore:nextera_legacy:i7 had 0 good hits.
INFO:explore:Adaptor nextera_legacy is excluded from the analysis
INFO:explore:Parsing nextera_dual
INFO:explore:nextera_dual:i5 had 0 good hits.
INFO:explore:nextera_dual:i7 had 0 good hits.
INFO:explore:Adaptor nextera_dual is excluded from the analysis
INFO:explore:illumina_ud:i5 had 113979 good hits with median insert length 10.0
INFO:explore:insert_len
4.0          9
5.0         53
6.0        128
7.0        336
8.0        879
9.0       3144
10.0    106083
11.0      2183
12.0       709
13.0       299
14.0       102
15.0        29
16.0        13
17.0         5
18.0         5
19.0         1
21.0         1
Name: count, dtype: int64
INFO:explore:illumina_ud:i7 had 203160 good hits with median insert length 10.0
INFO:explore:insert_len
4.0         14
5.0         58
6.0        193
7.0        540
8.0       1486
9.0       5636
10.0    189757
11.0      3700
12.0      1066
13.0       449
14.0       169
15.0        49
16.0        27
17.0         7
18.0         5
19.0         2
20.0         1
21.0         1
Name: count, dtype: int64

[alneberg]

@remiolsen this should be ready to have a look at now. The explore command is just experimental in this PR and then we can keep making it better integrated into anglerfish later.

[remiolsen]

I think this tool is looking very promising as is now. Only a handful of comments, but I am very happy to merge this.