Num Intervening does not always produce result

[monprin]

When calling the candidate_genes function with the include_num_intervening option, not all genes will necessarily get this attribute. For instance, when calling with a larger list (from the Sucrose term, in the ZmRoot network in the ZmWallace ontology), this gene:

    {'organism': 'Zea Mays', 'strand': '-', 'num_siblings': 3, 'ID': 'GRMZM2G143499', 'Name': 'GRMZM2G143499', 'biotype': 'protein_coding', 'intervening_rank': 1.0, 'build': '5b', 'parent_locus': '<None>10:145891859-145891859'}

Does not receive the the num_intervening attribute and thus can cause failure.

The relevant section of code can be found in RefGen.py lines 455-468.

[monprin]

More info about the offending gene:

    id: GRMZM2G143499
    chrom: 10
    start: 145891859
    end: 145895272
    snp: 10:145891859-145891859
    ldegree: 1
    gdegree: 70
    locality: 0.014285714285714285
    num_intervening: NAN
    rank_intervening: 1.0
    num_siblings: 3

[schae234]

Not sure where this error is occurring, here is what I see:

In [34]: import camoco as co
In [35]: snp = co.Locus(10,145891859,145891859)
In [36]: Zm5bFGS = co.RefGen('Zm5bFGS')
In [37]: gene = Zm5bFGS['GRMZM2G143499']
In [38]: snp in gene
Out[38]: True

If that is true, then this:

            if include_num_intervening == True:                                 
                num_down = 0                                                    
                num_up = 0                                                      
                # Sort the genes by their distance from the locus               
                genes = sorted(genes,key=lambda x: x-locus)                     
                for gene in genes:                                              
                    if locus in gene:                                           
                        gene.update({'num_intervening':-1})                     
                    elif gene > locus:                                          
                        gene.update({'num_intervening':num_down})               
                        num_down += 1                                           
                    elif gene < locus:                                          
                        gene.update({'num_intervening':num_up})                 
                        num_up += 1 

should have num_intervening be -1.

[monprin]

Well I am about to embark on upgrading camoco to your version, so it might be old, I will do that and see if it is still a problem.