Questions tagged [parsing]
The parsing tag has no usage guidance.
13
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Print indel/mismatch in a blastp stream
I am in need of a simple tool that accepts an XML file generated by a BlastP as input and gives me back a file containing information about mismatches/indels/etc. Fortunately such a tool already ...
- 11
2
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2
answers
384
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Parsing a genbank file and outputting specific feature information to a csv using BioPython
So I am trying to parse through a genbank file, extract particular feature information and output that information to a csv file. The example genbank file looks like this:
SBxxxxxx.LargeContigs.gbk
<...
- 101
2
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1
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94
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Parsing text within a taxonomy.csv file
I have the following file in tab separated values (TSV).
ID
Taxonomy
76980f6d906c6baaef3f96559fc7ba1b
d__Eukaryota; p__Cercozoa; c__Vampyrellidae; o__Vampyrellidae; f__Vampyrellidae; g__uncultured
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1
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1
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754
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How to extract residues from specific chain of interest from multiple pdb files?
I'm new to biopython & I'm trying to extract residues from specific chain of each file from a list of 316 pdb files. Eg: 1d8t has four chains A, B, C & D of which my interest is to extract ...
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1
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1
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3k
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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 ...
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4
votes
1
answer
477
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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 I've found a solution but the code is outdated:
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- 51
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0
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629
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GTF parser for Python
I found this GTF parser for Python. However, it does not work with Scallop's GTF file:
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- 453
1
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2
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76
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tabix indexing a GTEx variant file- ':' delimited
I have a gtex variant file- the head of which looks as follows:
...
- 111
0
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1
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92
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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.
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- 1,754
1
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0
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39
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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 ...
- 11
2
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2
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95
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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 ...
- 21
2
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2
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719
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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 ...
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4
votes
2
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542
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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 ...
- 375