Iteration error on result of groupby about pybedtools HOT 5 CLOSED

you can probably get around this by adding the full=True kwarg to the groupby method.

you can also iterate over the result of the grouping outside of bedtools as:

for line in open(grouped_bed.fn):
     stuff = line.split("\t")
     ...

from pybedtools.

As Brent points out, full=True does the trick for this case.

Under the hood, there's a bunch of checking to see how many fields there are in a line, if it looks like GFF or not, which fields can be converted to an integer, and so on. Then Interval objects are created with a appropriate chrom/start/stop etc attributes and 0- or 1-based coordinates.

For the general case, I'd prefer not to support arbitrarily-formatted (though created by BEDTools) formats like this. But you could write a converter -- if full=True wasn't an option, then you could modify the last two lines of your example to yield lines that are in fact BED-like:

def reformat(x):
    for line in open(x.fn):
        fields = line.strip().split('\t')
        yield pybedtools.create_interval_from_list([
            fields[1], fields[2], fields[3], fields[0], fields[4], fields[5]])

for line in reformat(grouped_bed):
    print line.fields

from pybedtools.

Thanks so much Brent and Ryan, I didn't think to use .fn (I guess it's technically only there temporarily right?) and totally missed full=True. Very helpful, thanks!

from pybedtools.

Yep, if you don't do anything special, .fn will be deleted when the interpreter exits. But you could use a .saveas() call if you want to save it for later. Alternatively, when running groupby() (or any method that wraps BEDTools commands), use the output kwarg to have it save the file to a specific filename.

from pybedtools.

Is there a "smart" way to get a bed format back from this groupyby?

bed.groupby(
    g=[9], 
    c=[1,        2,      3,       4,     5,      6,       7,       8,      9], 
    o=['first', 'first', 'first', 'min', 'max', 'first', 'first', 'first', 'first'], 
)

Result:

ID=AT1G01010;	Chr1	Araport11	five_prime_UTR	1131	6130	.	+	.	ID=AT1G01010;
ID=AT1G01020;	Chr1	Araport11	five_prime_UTR	5965	11630	.	-	.	ID=AT1G01020;
ID=AT1G01030;	Chr1	Araport11	five_prime_UTR	10674	16214	.	-	.	ID=AT1G01030;
ID=AT1G01040;	Chr1	Araport11	five_prime_UTR	20621	25915	.	+	.	ID=AT1G01040;
ID=AT1G01050;	Chr1	Araport11	five_prime_UTR	30510	35671	.	-	.	ID=AT1G01050;
ID=AT1G01060;	Chr1	Araport11	five_prime_UTR	34422	40371	.	-	.	ID=AT1G01060;
ID=AT1G01070;	Chr1	Araport11	five_prime_UTR	38446	43517	.	-	.	ID=AT1G01070;
ID=AT1G01080;	Chr1	Araport11	five_prime_UTR	44520	49559	.	-	.	ID=AT1G01080;
ID=AT1G01090;	Chr1	Araport11	five_prime_UTR	46805	51804	.	-	.	ID=AT1G01090;
ID=AT1G01100;	Chr1	Araport11	five_prime_UTR	48464	53710	.	-	.	ID=AT1G01100;

Aside from the grouping column (first column in the output), the output should be valid bed, but when I tried to use cut to remove the first column, I got the same MalformedBedLineError error as in this issue. (As an aside, this was not obvious to me, as the documentation for cut says "returns a BedTool of results [...] indexes returned must be valid GFF/GTF/BED/SAM features", not that the input needs to be valid features).

I can use the reformat code given above, but maybe there is a more straight forward solution?

from pybedtools.