[Biopython] Updating feature Location in Seqfiles

"F.L. Ratzkowski" <[email protected]> Wed, 11 Nov 2020 17:20:08 +0000
Newsgroups gmane.comp.python.bio.general
Message-ID <LNXP265MB1209FD8F61313E13F39BC226FBE80@LNXP265MB1209.GBRP265.PROD.OUTLOOK.COM>
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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