Questions tagged [parsing]

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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 ...
Eduardo M.'s user avatar
2 votes
2 answers

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 <...
Joe_G's user avatar
  • 101
2 votes
1 answer

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 ...
Marco's user avatar
  • 151
1 vote
1 answer

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 ...
Husna Riyaz's user avatar
1 vote
1 answer

#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 ...
Hong's user avatar
  • 21
4 votes
1 answer

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 I've found a solution but the code is outdated: ...
raysteven's user avatar
0 votes
0 answers

GTF parser for Python

I found this GTF parser for Python. However, it does not work with Scallop's GTF file: ...
user977828's user avatar
1 vote
2 answers

tabix indexing a GTEx variant file- ':' delimited

I have a gtex variant file- the head of which looks as follows: ...
which_command's user avatar
0 votes
1 answer

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. ...
kcm's user avatar
  • 1,754
1 vote
0 answers

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 ...
revl's user avatar
  • 11
2 votes
2 answers

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 ...
kathirvel k's user avatar
2 votes
2 answers

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 ...
Andrea Spinelli's user avatar
4 votes
2 answers

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 ...
andresito's user avatar
  • 375