{ "info": { "author": "Sebastien Briois, Guillaume Tiberi", "author_email": "sebriois@gmail.com", "bugtrack_url": null, "classifiers": [ "Environment :: Web Environment", "Intended Audience :: Developers", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# bioinfo_tools 0.3.1\n\n## Installation\n\n```bash\npip install bioinfo_tools\n```\n\n## Parsers\n\n*HEADS UP!* These parsers are still under development and usage is not consistent from one parser to another.\n\n### Fasta parser\n\n```python\nfrom bioinfo_tools.parsers.fasta import FastaParser\n\nfasta_parser = FastaParser()\n\n# by default, sequence IDs are separated by the firstly found '|' or ':'\nfor seqid, sequence in fasta_parser.read(\"/path/to/file.fasta\"):\n print(seqid, sequence)\n\n# you may specify a specific separator for your sequence ID (e.g white space):\nfor seqid, sequence in fasta_parser.read(\"/path/to/file.fasta\", id_separator=\" \"):\n print(seqid, sequence)\n```\n\n### GFF parser\n\n```python\nfrom bioinfo_tools.parsers.gff import Gff3\n\ngff_parser = Gff3()\nwith open(\"/path/to/file.gff\", \"r\") as fh:\n for gene in gff_parser.read(fh):\n print(gene)\n\nimport gzip\nwith gzip.open(\"/path/to/file.gz\", \"rb\") as fh:\n for gene in gff_parser.read(fh):\n print(gene)\n```\n\n### OBO parser\n\n\n```python\nfrom bioinfo_tools.parsers.obo import OboParser\n\nobo_parser = OboParser()\nwith open(\"/path/to/file.obo\") as fh:\n go_terms = obo_parser.read(fh)\n\nfor go_term in go_terms.values():\n print(go_term)\n\n # you may also get the GO term parents via the parser\n parents = obo_parser.get_parents(go_term)\n```\n\n## Usage Examples\n\n### Extract all introns sequences by parsing GFF and fasta files\n\nIn this example, we focus on a genome assembly. We will first load a GFF file containing gene annotations for this\nassembly, then load a fastA file containing the nucleic sequences of each chromosome in the genome.\nWe will then collect all transcript introns and extract their nucleic sequences.\n\n**__DISCLAIMER__**: for this example to work, your GFF file must expose at least the following feature types in column #3:\n - `gene`\n - one of `transcript|mRNA|RNA` (or lowercased version)\n\n\n```python\nfrom bioinfo_tools.genomic_features.chromosome import Chromosome\nfrom bioinfo_tools.parsers.gff import Gff3\nfrom bioinfo_tools.parsers.fasta import FastaParser\n\nchromosomes = dict() # {: }\n\n# start with parsing a GFF file\ngff_parser = Gff3()\nwith open(\"/path/to/gene_models.gff\", \"r\") as fh:\n for gene in gff_parser.read(fh):\n chromosome = gene['seqid']\n\n if chromosome not in chromosomes:\n chromosomes[chromosome] = Chromosome(chromosome) # init a new Chromosome object\n\n chromosomes[chromosome].add_gene(gene) # add the current gene to our Chromosome object\n\n# load our chromosome sequences in memory\nfasta_parser = FastaParser()\nfor chromosome, nucleic_sequence in fasta_parser.read(\"/path/to/genome_chromosomes.fasta\"):\n if chromosome not in chromosomes:\n chromosomes[chromosome] = Chromosome(chromosome)\n # attach parsed chromosome sequence to our Chromosome object\n chromosomes[chromosome].attach_nucleic_sequence(nucleic_sequence)\n\n# now, collect introns and extact their nucleic sequence\nintrons_sequences = dict() # {: }\nfor chromosome in chromosomes.values():\n for gene in chromosome.genes:\n for transcript in gene.transcripts:\n for idx, intron in enumerate(transcript.introns):\n intron_id = \"%s_intron_%s\" % (transcript.transcript_id, idx)\n intron_seq = intron.extract(chromosome.nucleic_sequence) # that we attached above\n introns_sequences[intron_id] = intron_seq\n\n# from here, you can do what you want with the intron sequences (eg. write them to a fasta file, etc)\n# 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