Index error in python
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Entering edit mode
18 months ago

Dear all,

When I run a Python script, it reported an error like this:

Traceback (most recent call last):
  File "replace_gff_gene_id.py", line 7, in <module>
    ab[lst1[0]] = lst1[1]
IndexError: list index out of range

The whole script is like this:

python replace_gff_gene_id.py Prunella_fulvescens_BGI_coress.seqid Prunella_fulvescens.homolog.gff > Prunella_fulvescens.modify.gff3

Also attached script replace_gff_gene_id.py here:

import sys

ab = {}
with open(sys.argv[1]) as  rename_file:
    for row in rename_file:
        lst1 = row.strip().split('\t')
        ab[lst1[0]] = lst1[1]
#print(ab)

with open(sys.argv[2]) as gff_file:
    for row in gff_file:
        for key,value in ab.items():
            row = row.replace(key,value).strip()
        print(row)

Here is an example for input file 1, Prunella_fulvescens_BGI_coress.seqid:

PRUFUL_R14685   Prunella_himalayana_BGI_1
PRUFUL_R05501   Prunella_himalayana_BGI_2
PRUFUL_R10205   Prunella_himalayana_BGI_3
PRUFUL_R07295   Prunella_himalayana_BGI_4
PRUFUL_R07296   Prunella_himalayana_BGI_5
PRUFUL_R10726   Prunella_himalayana_BGI_6
PRUFUL_R13095   Prunella_himalayana_BGI_7
PRUFUL_R13096   Prunella_himalayana_BGI_8
PRUFUL_R14411   Prunella_himalayana_BGI_9
PRUFUL_R07297   Prunella_himalayana_BGI_10

Here is an example for input file 2, Prunella_fulvescens.homolog.gff:

scaffold9610    GeneWise    mRNA    732 962 54.88   -   .   ID=PRUFUL_R00001;Source=ENSTGUP00000017881-D17;Shift=0;MidStop=0;
scaffold9610    GeneWise    CDS 732 962 .   -   0   Parent=PRUFUL_R00001;Source=ENSTGUP00000017881-D17;
scaffold9610    GeneWise    mRNA    2503    2764    74.71   -   .   ID=PRUFUL_R00002;Source=ENSTGUP00000018017-D16;Shift=1;2653-2656;MidStop=0;
scaffold9610    GeneWise    CDS 2503    2652    .   -   0   Parent=PRUFUL_R00002;Source=ENSTGUP00000018017-D16;
scaffold9610    GeneWise    CDS 2657    2764    .   -   0   Parent=PRUFUL_R00002;Source=ENSTGUP00000018017-D16;
scaffold9610    GeneWise    mRNA    2081    2496    63.16   -   .   ID=PRUFUL_R00003;Source=ENSTGUP00000018035-D83;Shift=0;MidStop=0;
scaffold9610    GeneWise    CDS 2081    2195    .   -   1   Parent=PRUFUL_R00003;Source=ENSTGUP00000018035-D83;
scaffold9610    GeneWise    CDS 2246    2496    .   -   0   Parent=PRUFUL_R00003;Source=ENSTGUP00000018035-D83;

I would be very appreciated if you could help fixing this issue

Python • 653 views
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Entering edit mode

Impossible to answer without posting at least an example of the input file.

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Entering edit mode

Thanks for the reply! I updated and posted the examples for input files~

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Double check that tab is actually the field separator for the input file. List goes out of range because splitting by tab results in a single field (only index 0). Provided code has no problem at all.

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