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View Code? Open in Web Editor NEWA series of small Biopython scripts for downloading sequence data off NCBI's Genbank.
License: MIT License
A series of small Biopython scripts for downloading sequence data off NCBI's Genbank.
License: MIT License
Uses:
for x in range(0, len(SeqRecords)): <--- is redundant.
Could use:
for x in SeqRecords: <--- simpler cleaner
Uses:
for x in range(0, len(SeqRecords)): <--- is redundant.
Could use:
for x in SeqRecords: <--- simpler cleaner
handle = Entrez.efetch(db="protein", id=seqList, rettype="gb", retmode="genbank")
Enterz.efetch queries protein database not nucleotide.
Hasn't caused any problems yet. Even if I give it nucleotide sequences.
Biopython/enterz.efetch issue with certain accession listed. Seems to effect all compete refseq accessions and some shotgun sequenced Refseq accessions.
List of effected accessions:
NC_008268
NC_012490
NC_012522
NC_014659
NC_022115
NC_023150
NZ_AGVD00000000
NZ_AJFC00000000
Example Accessions:
CP006996.1
AOHP00000000.1
ALQA00000000.1
ANIU00000000.1
Regexes in individual methods can be pulled out so they are only compiled once?
Potential efficiency enhancement?
extractContigs() should use the sequence record object's methods rather than parsing the string. A possible approach is sequence to use the sequence record object's annotations dictionary.
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