Questions tagged [parsing]

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#1 Parsing trouble java.lang.NumberFormatException in GSEA 4.2.1

I am getting the following error message when I tried to load .TXT data file to GSEA 4.2.1. I tried different way to change the file name as .GCT but not working. Any suggestion? Many thanks. Full ...
3
votes
1answer
61 views

Updating the GFF3 + Fasta to GeneBank code

I'm trying to convert gff3 and fasta into a gbk file for usage in Mauve. I've found a solution but the code is outdated: ...
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0answers
264 views

GTF parser for Python

I found this GTF parser for Python. However, it does not work with Scallop's GTF file: ...
1
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2answers
49 views

tabix indexing a GTEx variant file- ':' delimited

I have a gtex variant file- the head of which looks as follows: ...
0
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1answer
59 views

europmc and tidypmc R library for extracting or making metadata from publication

I'm trying to use this europmc r libray where I have a list of pmids to look for. I tried with pubtator but its bit complicated.In Europmc i can all the annotated terms etc. ...
0
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0answers
26 views

VCF spec: is it possible to have other alleles in addition to the MISSING value ('.') in ALTS?

I'm writing a VCF parser, so I have to consider and handle all corner cases regardless of how contrived they may seem. The specification is a bit unclear about the MISSING value ('.') in the ALTS ...
2
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2answers
74 views

How to remove sequence reads contains more than 2 X from multifasta file?

I have 5000 protein sequences in one multifasta file. I found more reads have gaps as X in their reads. So, want to eliminate those reads completely (Whole protein seq) from the file. I am keeping ...
2
votes
1answer
428 views

Biopython - extracting query coverage from XML Blast output

I need to extract (or to calculate precisely) the query coverage from Blast output. I am using NCBIWWW.qblast to query Blast in XML format. Is it possible to know the query coverage parsing the XML ...
4
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2answers
395 views

Transform traditional blast output to `--outfmt 6`

I have run a blastx of metagenomic databases (raw illumina reads) using the nr database. Unfortunately, I forgot to add the --outfmt 6 argument to the code and got ...