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Copy file name to clipboardExpand all lines: docs/_build/html/_sources/pm-doc.rst.txt
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@@ -91,12 +91,16 @@ Note that the prefix 'test' entered with the -o (output) argument became the pre
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Parent-map can also bypass the sequence analysis and just colorize an existing -par.txt file into a -par.html file. This is useful when the user is not satisfied with the default colors and wants to try different color schemes. In this case, the -C argument is used followed by the name of the -par.txt file. Also, the -p argument must be used followed by a list of parent color pairs. Example::
The following output will be generated, while the newly created html file is automatically displayed (thanks to option -d) in the default web browser::
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Colorized version of parental map file saved into file: test-par.html
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A portion of the generated html file is shown here:
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.. image:: _static/SCH9.png
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Arguments
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*********
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#. **Other**:
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Number of sequence positions that could not be matched to any parent and could not be considered as a variation of one particular parent.
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Example of a -stats.txt file:
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.. image:: _static/stats.png
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Parental mapping
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****************
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In the -par.txt file, each variant complete sequence is displayed along its contributing parental fragments. The parental mapping is simplified as much as possible, so that the variant is completely described using as few parents as possible and as few fragments as possible. Only the necessary parents are shown. If a fragment can be mapped equally to more than one parent, the parent that has the highest overall coverage is chosen. Identities are displayed in the parent lines using an identity symbol ('.' by default). If a mismatch occurs between 2 fragments mapped to the same parents or at a sequence end, it is considered a variation of the parent next to it and displayed as the parent sequence (substitution) or using the gap symbol ('-' by default) in the parent line for insertions or in the variant line for deletions. The -par.txt file is most useful for variant sequences selected from shuffled libraries. Two files are generated: a black and white text file (name ending with -par.txt) and a colorized html version of the same file (name ending with -par.html). In the html file, each parent name and its corresponding identity fragments are colorized using a different color (whenever possible). The default color scheme uses 12 different colors. If the number of parents in the file is greater than 12, the same set of 12 colors is used on the 12 next parents and so on. If the user wishes to apply specific colors, the :ref:`-p argument <colors>` needs to be used followed by a list of parent color pairs, either at the time of the sequence analysis or later with the -C argument to specify the -par.txt file to be colorized again.
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Example of a -par.txt file (showing AAV-DJ only)::
Same map from the corresponding -par.html file, using default colors:
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.. image:: _static/AAV-DJ.png
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Sequence definitions
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********************
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#. **Parent sequence**:
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In the case of substitutions or deletions, the corresponding parental sequence is displayed here.
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Here is an example of a -def.txt file::
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Variant name: OLIG001
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Variant region Parent/feature Parent region Variant sequence Parent sequence``
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1-124 AAV2 1-124
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86-156 AAV9 86-156
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136-178 AAV6 136-178
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165-262 AAV9 165-262
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234-341 AAV8 235-342
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333-373 AAV2 331-371
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343-531 AAV8 344-532
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532 substitution 533 K E
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533-725 AAV8 534-726
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726 unmatched H
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727-737 AAV6 726-736
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Variant name: AAV2i8
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Variant region Parent/feature Parent region Variant sequence Parent sequence
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1-584 AAV2 1-584
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582-590 AAV8 585-593
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591-735 AAV2 591-735
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Variant name: rAAV2-retro
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Variant region Parent/feature Parent region Variant sequence Parent sequence
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1-381 AAV2 1-381
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382 substitution 382 D N
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383-587 AAV2 383-587
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588-597 insertion 587/588 LADQDYTKTA
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598-717 AAV2 588-707
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718 substitution 708 I V
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719-745 AAV2 709-735``
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Alignments
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**********
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The -aln.txt file consists of two parts: the first concerns sequences derived from a single parent, while the second part is about sequences derived from multiple parents. In each part, variants derived from the same main parents are aligned together against their main parent. Only regions that differ from the parent in any of the variants are shown, and the region position is indicated by a number (numbering is the one defined in the parental sequence file as explained in :ref:`parents <parents>`). Sequence identity is shown using the identity symbol (default: '.'), gaps are shown using the gap symbol (default: '-'). Insertions are indicated by a gap in the parent sequence, deletions by a gap in the variant sequence. For substitutions, the actual sequence is shown. Increasing the region area (using the -e argument) allows to show more sequence context and to combine neighboring regions. The -aln.txt file is most useful for variants derived from a single parent (such as from insertion or targeted substitution libraries), as it allows to compare variants in discrete regions, which can be much larger in number and size when variants are derived from multiple parents (as in shuffled libraries).
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Example of -aln.txt file::
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Alignment of variant sequences against their main parental sequence - single parent
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