Output all network nodes and edges.

In some sort of format that makes sense. For now, going to copy the CRC program output formats so that downstream reporting/viz can be used with both. File names from the example data/run that I used are in parentheses.

[x] List of all node genes (genes marked by a (super)enhancer).
[x] List of all TF node genes (TF genes marked by a superenhancer).

[x] Full edge table (A549_CRCs_EDGE_TABLE.txt):

SOURCE  TARGET  CHROM   START   STOP    REGION_ID   TF_INTERACTION
ARNTL   ABHD2   chr15   89119809    89119818    Peak_382    0
ARNTL   AC002066.1  chr7    116354919   116354928   10_Peak_18966_lociStitched  0
ARNTL   AC004585.1  chr17   40518775    40518784    Peak_411    0
ARNTL   AC004585.1  chr17   40543266    40543275    Peak_411    0
ARNTL   AC004585.1  chr17   40551758    40551767    Peak_411    0
ARNTL   AC004585.1  chr17   40552457    40552466    Peak_411    0

This represents ARNTL motifs found in enhancers (and/or promoters?) of the genes in the "TARGET" column. This can be used to create dynamically network plots from one or more TFs as selected by the user, optionally limiting to TF-TF interactions as designated in the last column (1 indicates that it's a TF-TF regulatory interaction).

[ ] (Super) enhancer BED files (A549_CRCs_ENHANCER_TABLE.txt). Currently, this format looks like:

ENHANCER_ID CHROM   START   STOP    GENE_LIST
68_Peak_17995_lociStitched  chr5    58960811    59309427    PDE4D
31_Peak_11846_lociStitched  chr5    59459122    59621436    PDE4D
25_Peak_83063_lociStitched  chr5    172827953   172935578   ERGIC1,RPL26L1,ATP6V0E1,RF00019,AC008429.1
4_Peak_37549_lociStitched   chr15   98842601    98908710    IGF1R
Peak_411    chr17   40504195    40561897    AC004585.1,AC018629.1,TNS4

Last column is gene assignments. I kind of hate this format, switching to a BED-like format would be easier to worth with. Maybe add another column for whether it's a TF or not, which is currently subsetted into the (A549_CRCs_ENHANCER_TF_TABLE.txt) file.

[ ] List of self loops (A549_CRCs_SELF_LOOPS.txt), these are just TFs that have a motif in one of their own enhancers.
```
SOX2
JUN
EGR1
```
[ ] List of genes and their associated enhancers, and their TF designation (A549_CRCs_GENE_SUMMARY.txt). In the example data, it's only the SE-associated genes as the SEs were the only enhancers I provided:
```
GENE    TF  ENHANCER_LIST
AAK1    0   18_Peak_55661_lociStitched
ABCC1   0   16_Peak_3421_lociStitched
ABCC2   0   1_Peak_127_lociStitched
ABCC3   0   Peak_101,Peak_450,Peak_84
```

I feel it may be worth having two enhancer columns - one for super enhancers and one for "typical" enhancers.

This is still a WIP, will add more in a bit.

stjude-biohackathon / CRCminer

Output all network nodes and edges. #7