[Biopython] Updating feature Location in Seqfiles
F.L. Ratzkowski
flr28 at cam.ac.uk
Wed Nov 11 17:20:08 UTC 2020
Hi,
i am new here so I am sorry if I am doing anything wrong, feel free to tell me.
I am farely new to biopython as well, currently i have written a script that reads in a .gbk file and then deletes and inserts different parts of the sequence. this would alter the absolute position of features. I have ultimately run a script that safes the new positions in 2 dataframes. When i now want to update all features with the Featurelocation command it seems to not work. I saved the features in a variable before and after me updating the features and was hoping to then detect a difference but it fails. here the basic part of the script i am struggling with
CompareBefore = Seqfile.features
for z in range(0, len(featureEndList)):
feature_end = int(ELdf.iloc[z][1])
feature_start = int(SLdf.iloc[z][1])
feature_strand = Seqfile.features[z].location.strand
Seqfile.features[z].location = FeatureLocation(feature_start, feature_end,strand=feature_strand)
CompareAfter = Seqfile.features
list = []
for x in range(0,len(CompareAfter)):
if CompareBefore[x] != CompareAfter[x]:
list.append(x)
I get 0 hits in this list.
Please help 🙂 thank you
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