[Biopython-dev] [Bug 2809] New: Adding startswith and endswith methods to the Seq object
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Fri Apr 10 10:13:58 EDT 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2809
Summary: Adding startswith and endswith methods to the Seq object
Product: Biopython
Version: Not Applicable
Platform: All
OS/Version: All
Status: NEW
Severity: enhancement
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk
OtherBugsDependingO 2351
nThis:
As part of making the Seq object more like the Python string (Bug 2351), we
need alphabet aware startswith and endswith methods. Patch to follow.
There are many possible use cases for this. One example which prompted me to
work on this was taking SeqRecord objects from sequencing reads (a FASTQ file
read in with Bio.SeqIO) where some include a PCR primer associated
prefix/suffix which I want to strip off (by slicing the SeqRecord). To do this
I need to know if a given SeqRecord's sequence starts with (or ends with) a
given primer sequence (or tuple of primer sequences).
Current work around, str(record.seq).startswith(prefix)
Patch to follow, which will allow record.seq.startswith(prefix) directly.
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