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Optimised sequence conversion code (PRIVATE).
You are not expected to access this module, or any of its code, directly. This is all handled internally by the Bio.SeqIO.convert(...) function which is the public interface for this.
The idea here is rather while doing this will work:
from Bio import SeqIO records = SeqIO.parse(in_handle, in_format) count = SeqIO.write(records, out_handle, out_format)
it is shorter to write:
from Bio import SeqIO count = SeqIO.convert(in_handle, in_format, out_handle, out_format)
Also, the convert function can take a number of special case optimisations. This means that using Bio.SeqIO.convert() may be faster, as well as more convenient. All these file format specific optimisations are handled by this (private) module.
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_converter =
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__package__ =
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Fast Sanger FASTQ to Sanger FASTQ conversion (PRIVATE). Useful for removing line wrapping and the redundant second identifier on the plus lines. Will check also check the quality string is valid. Avoids creating SeqRecord and Seq objects in order to speed up this conversion. |
Fast Solexa FASTQ to Solexa FASTQ conversion (PRIVATE). Useful for removing line wrapping and the redundant second identifier on the plus lines. Will check also check the quality string is valid. Avoids creating SeqRecord and Seq objects in order to speed up this conversion. |
Fast Illumina 1.3+ FASTQ to Illumina 1.3+ FASTQ conversion (PRIVATE). Useful for removing line wrapping and the redundant second identifier on the plus lines. Will check also check the quality string is valid. Avoids creating SeqRecord and Seq objects in order to speed up this conversion. |
Fast Illumina 1.3+ FASTQ to Sanger FASTQ conversion (PRIVATE). Avoids creating SeqRecord and Seq objects in order to speed up this conversion. |
Fast Sanger FASTQ to Illumina 1.3+ FASTQ conversion (PRIVATE). Avoids creating SeqRecord and Seq objects in order to speed up this conversion. Will issue a warning if the scores had to be truncated at 62 (maximum possible in the Illumina 1.3+ FASTQ format) |
Fast Solexa FASTQ to Sanger FASTQ conversion (PRIVATE). Avoids creating SeqRecord and Seq objects in order to speed up this conversion. |
Fast Sanger FASTQ to Solexa FASTQ conversion (PRIVATE). Avoids creating SeqRecord and Seq objects in order to speed up this conversion. Will issue a warning if the scores had to be truncated at 62 (maximum possible in the Solexa FASTQ format) |
Fast Solexa FASTQ to Illumina 1.3+ FASTQ conversion (PRIVATE). Avoids creating SeqRecord and Seq objects in order to speed up this conversion. |
Fast Illumina 1.3+ FASTQ to Solexa FASTQ conversion (PRIVATE). Avoids creating SeqRecord and Seq objects in order to speed up this conversion. |
Fast FASTQ to FASTA conversion (PRIVATE). Avoids dealing with the FASTQ quality encoding, and creating SeqRecord and Seq objects in order to speed up this conversion. NOTE - This does NOT check the characters used in the FASTQ quality string are valid! |
Fast FASTQ to simple tabbed conversion (PRIVATE). Avoids dealing with the FASTQ quality encoding, and creating SeqRecord and Seq objects in order to speed up this conversion. NOTE - This does NOT check the characters used in the FASTQ quality string are valid! |
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_converter
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