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Adding Features to a GenBank File - Any Help?

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  • Adding Features to a GenBank File - Any Help?

    Hi all!

    I'm currently working with a multi entry genbank file and two dataframes in order to add new qualifiers to the genbank file via its key/value system.

    Each entry is a contig, and so far I am able to add new keys on top of the already existing "locus_tag" and "translation" for each entry. However, I am having some difficulties adding values from the dataframes to each contigs.

    Each dataframe is made of 3 columns but holds 6000+ lines of data. I am able to insert one specific column into the genbank file, but these 6000 lines print for every contig.

    I've tried making a for loop, but the 6000 lines continue to print and I am not sure what else to do. Any help would be greatly appreciated!


    This is the code I am working with:

    import os
    from Bio.Seq import Seq
    from Bio.SeqRecord import SeqRecord
    from Bio.SeqFeature import SeqFeature, FeatureLocation
    from Bio import SeqIO
    import pandas as pd
    df1 = pd.read_csv("-f_besthit.csv")
    df2 = pd.read_csv("-f_filtered.csv")
    annotation_handle = open("META.gbk","r")
    recs = [rec for rec in SeqIO.parse("META.gbk", "genbank")]
    my_start_pos = (2)
    my_end_pos = (6)
    my_feature_location = FeatureLocation(my_start_pos,my_end_pos)
    for rec in recs:

    my_feature_type = "CDS"
    full_product={"full_product":"df_best[full_product]","complement":"(1..423)", "locus_tag":"contig", "besthit":"df_fil[besthit]"}
    my_feature = SeqFeature(my_feature_location,type=my_feature_type, qualifiers=full_product)
    besthit={"besthit":"df_fil[besthit]"}
    my_feature_one = SeqFeature(my_feature_location,type=my_feature_type, qualifiers=besthit)

    rec.features.append(my_feature)
    feats = [feat for feat in rec.features if feat.type == "CDS"]
    for feat in feats:
    print(feat)
    for record in SeqIO.parse(annotation_handle,"genbank"):

    a = len(record.features)

    for_rast = open("META.gbk","w")
    x = 0
    final_features = []

    for f in record.features:
    if f.type == "CDS":
    f.qualifiers["full_product"] = "%s_%s" % (df2.loc[:,"besthit"], x+1)
    x += 1
    for f in record.features:
    if f.qualifiers["full_product"] == df2.loc[:"orf"]:
    final_features.append(f)
    else:
    pass


    record.features = final_features
    with open("META.gbk","w") as for_rast:
    SeqIO.write(record, for_rast, "genbank")
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