使用biopython处理gff文件

Question

I have a GFF file , which is a tab limited 9 column file. My Gff file looks like this :

chr1    GenBank region  1   2821361 .   +   1   ID=CP000253.1
chr1    S-MART  utr5    313 516     .   +   .   ID=CP000253.1|+313..516
chr1    GenBank gene    517 1878    .   +   1   ID=SAOUHSC_00001

......... and so on.

Problem Statement :

Now , I want to merge the rows which satisfy a condition. The condition is the 5th column value of ith row should be equal to 4th column of the i+1 row minus 1.

so the final result should be like

chr1    GenBank region  1   2821361 .   +   1   ID=CP000253.1
chr1    predict TU      313 1878    .   +   1   ID=SAOUHSC_00001

To do this, I wrote the following program:

from BCBio import GFF
from Bio.SeqFeature import SeqFeature, FeatureLocation

in_file = "infile.gff"
out_file = "outfile.gff"

limit_info = dict(
        gff_type = ['CDS','exon','gene','mRNA','operon','rRNA','tRNA','utr3','utr5'])
new_qualifiers = {"source": "prediction","ID": "CP000253.1"}
new_sub_qualifiers = {"source": "prediction"}
new_top_feature = SeqFeature(FeatureLocation(0, 2821361), type="genomeRegion", strand=1,
                         qualifiers=new_qualifiers)
i=0

in_handle = open(in_file)
for rec in GFF.parse(in_handle, limit_info=limit_info):
    for i in range(10):
        if rec.features[i].location.end == rec.features[i+1].location.start :
            # print rec.features[i]
            new_top_feature.sub_features[i] =     
[SeqFeature(FeatureLocation(rec.features[i].location.start ,  
rec.features[i+1].location.end ,strand=rec.features[i].strand),  
type="Transcription_unit",  qualifiers=new_sub_qualifiers)]             

in_handle.close()

rec.features = [new_top_feature]

with open(out_file, "w") as out_handle:
    GFF.write([rec], out_handle)

I get the following error :

/usr/lib/python2.7/dist-packages/Bio/SeqFeature.py:171: BiopythonDeprecationWarning: Rather using f.sub_features, f.location should be a CompoundFeatureLocation
  BiopythonDeprecationWarning)
Traceback (most recent call last):
  File "/home/nkumar/workplacekepler/random/src/limit.py", line 26, in <module>
    new_top_feature.sub_features[i] = [SeqFeature(FeatureLocation(rec.features[i].location.start , rec.features[i+1].location.end ,strand=rec.features[i].strand), type="Transcription_unit",  qualifiers=new_sub_qualifiers)]
IndexError: list assignment index out of range

Even though it is a index out of range error, I am not able to figure out , what is wrong?

in_handle = open(in_file)
for rec in GFF.parse(in_handle, limit_info=limit_info):
    for i in range(10):        
        if rec.features[i].location.end == rec.features[i+1].location.start :
            print 1          
        else:
            print rec.features[i]            
in_handle.close()

This one works perfectly and prints all the features.

Answer 1

You defined new_top_feature as:

type: genomeRegion
location: [0:2821361](+)
qualifiers: 
    Key: ID, Value: CP000253.1
    Key: source, Value: prediction

But it has not subfeatures

>>> print new_top_feature.sub_features
[]

new_top_feature.sub_features is thus an empty list. You can not assign to an empty list directly:

>>> a = []
>>> a[0] = 3
Traceback (most recent call last):
  File "<input>", line 1, in <module>
IndexError: list assignment index out of range

And this is what you are doing in

new_top_feature.sub_features[i] =  .....

To add data to this list you shoud use append instead than indexing. In case you need to fill the list at given positions in aleatory order, you could create a list of the adequate size filled with zeros and then assign the values to the positions as they come.