https://github.com/gedankenstuecke/bioinf-junk

Mainly simple & stupid text-parsers for blast-jobs
https://github.com/gedankenstuecke/bioinf-junk

Last synced: about 2 months ago
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Mainly simple & stupid text-parsers for blast-jobs

• Host: GitHub
• URL: https://github.com/gedankenstuecke/bioinf-junk
• Owner: gedankenstuecke
• Created: 2011-05-16T17:32:21.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2012-01-09T22:51:32.000Z (almost 13 years ago)
• Last Synced: 2024-06-11T16:25:59.262Z (7 months ago)
• Language: Python
• Homepage:
• Size: 2.74 MB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README

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README

        
Contents:

* misa -> Wrapper that uses misa to detect SSRs and gives back tab-delimited file with original-sequence

* utr_filter.py -> split a fasta-file into 2, one with all CDSs and one with all UTRs. Needs ORFPREDICTOR-Input

* radtag_finder.py -> Find all restriction-enzyme-sites in all sequences of a fasta-file

* snp_finder.py -> Find all SNPs in a BAM/SAM-File. SNPs are defined by minimum read depth of the alignment and the minimum allele frequency

* snp_utr_filter.py -> Bin SNPs to UTR/CDS-bins

* xml_blast_extractor.py -> parses blast-xml-output (useful if you want to use blast2go) and gives back a tab-delimited file incl. most important information about hits. use an evalue-cutoff to filter the hits

* readfilterfiter.py -> filter a huge fasta-file using sequence-identifiers to get rid of unwanted entries

* gofinder.py -> enhance cli-output of blast2go with more information about go-hits

* genreconstruction.py -> let's not talk about this one...

feel free to help or to tell me about bugs