Breaks up a EMBL file into SeqRecord objects for each CDS feature.

Every section from the LOCUS line to the terminating // can contain many CDS features. These are returned as with the stated amino acid translation sequence (if given).

Breaks up an EMBL file into SeqRecord objects.

Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features.

Note that for genomes or chromosomes, there is typically only one record.

This gets called internally by Bio.SeqIO for the EMBL file format:

 >>> from Bio import SeqIO
 >>> for record in SeqIO.parse("EMBL/epo_prt_selection.embl", "embl"):
 ...     print(record.id)
 ...
 A00022.1
 A00028.1
 A00031.1
 A00034.1
 A00060.1
 A00071.1
 A00072.1
 A00078.1
 CQ797900.1

Equivalently,

 >>> with open("EMBL/epo_prt_selection.embl") as handle:
 ...     for record in EmblIterator(handle):
 ...         print(record.id)
 ...
 A00022.1
 A00028.1
 A00031.1
 A00034.1
 A00060.1
 A00071.1
 A00072.1
 A00078.1
 CQ797900.1

Breaks up a Genbank file into SeqRecord objects for each CDS feature.

Every section from the LOCUS line to the terminating // can contain many CDS features. These are returned as with the stated amino acid translation sequence (if given).

Breaks up a Genbank file into SeqRecord objects.

Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features.

Note that for genomes or chromosomes, there is typically only one record.

This gets called internally by Bio.SeqIO for the GenBank file format:

 >>> from Bio import SeqIO
 >>> for record in SeqIO.parse("GenBank/cor6_6.gb", "gb"):
 ...     print(record.id)
 ...
 X55053.1
 X62281.1
 M81224.1
 AJ237582.1
 L31939.1
 AF297471.1

Equivalently,

 >>> with open("GenBank/cor6_6.gb") as handle:
 ...     for record in GenBankIterator(handle):
 ...         print(record.id)
 ...
 X55053.1
 X62281.1
 M81224.1
 AJ237582.1
 L31939.1
 AF297471.1

Breaks up an IMGT file into SeqRecord objects.

Every section from the LOCUS line to the terminating // becomes a single SeqRecord with associated annotation and features.

Note that for genomes or chromosomes, there is typically only one record.

Build a GenBank/EMBL position string (PRIVATE).

Use offset=1 to add one to convert a start position from python counting.

Build a GenBank/EMBL location from a (Compound) FeatureLocation (PRIVATE).

There is a choice of how to show joins on the reverse complement strand, GenBank used “complement(join(1,10),(20,100))” while EMBL used to use “join(complement(20,100),complement(1,10))” instead (but appears to have now adopted the GenBank convention). Notice that the order of the entries is reversed! This function therefore uses the first form. In this situation we expect the CompoundFeatureLocation and its parts to all be marked as strand == -1, and to be in the order 19:100 then 0:10.