New export fields. V5BeginTrimmed naming fixed. Docs.

milaboratory · Sep 25, 2015 · 622b80f · 622b80f
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diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT
@@ -1,5 +1,6 @@
 New feature: optional short column names in `export...` action to simplify further data analysis using data table processing libraries like Pandas or R/DataFrames. (`-s` / `--no-spaces` in `exportAlignments` and `exportClones`)
-Added `UTR5BeginTrimmed` reference point
+New export fields: `-defaultAnchorPoints` outputs positions of default anchor point in aligned reads or clonal sequence (this column is added to default output format), `-positionOf` outputs position of specified anchor point, `-lengthOf` outputs lengt of specified gene feature
+Added `V5UTRBeginTrimmed` anchor point, `V5UTR` gene feature renamed to `V5UTRGermline`, trimmed `V5UTR` gene feature added
 minor: some column names in output tab-delimited files slightly changed
 minor: NPE in exportAlignmentsPretty fixed
-minor: New reference poins added to exportAlignmentsPretty output
+minor: New anchor poins added to exportAlignmentsPretty output
diff --git a/doc/export.rst b/doc/export.rst
@@ -146,6 +146,16 @@ The following fields can be exported both for alignments and clones:
 +-----------------------------------+----------------------------------------------------------+
 | ``-minFeatureQuality [feature]``  | Minimal quality of sequence of specified gene feature.   |
 +-----------------------------------+----------------------------------------------------------+
+| ``-defaultAnchorPoints``          | Outputs a list of default anchor points (see table       |
+|                                   | below for the list of anchor points and format).         |
++-----------------------------------+----------------------------------------------------------+
+| ``-lengthOf [feature]``           | Outputs length of specified gene feature.                |
++-----------------------------------+----------------------------------------------------------+
+| ``-positionOf [anchorPoint]``     | Outputs position of specified anchor point in the        |
+|                                   | clonal sequence or aligned read.                         |
++-----------------------------------+----------------------------------------------------------+
+
+
 
 The following fields are specific for alignments:
 
@@ -183,6 +193,73 @@ The following fields are specific for clones:
 | ``-targets``  | Number of targets, i.e. number of gene regions used to assemble clones.                |
 +---------------+----------------------------------------------------------------------------------------+
 
+Default anchor point positions
+------------------------------
+
+Positions of anchor poins produced by ``-defaultAnchorPoints`` option are outputted as a colon separated list.
+If anchor point is not covered by target sequence nothing is printed for it, but flanking colon symbols are
+preserved to maintain positions in array. See example:
+
+::
+
+    :::::::::108:117:125:152:186:213:243:244:
+
+If there are several target sequences (e.g. paired-end reads or multi-part clonal sequnce), the array is outputted for
+each target sequence. In this case arrays are sepparated by comma:
+
+::
+
+    2:61:107:107:118:::::::::::::,:::::::::103:112:120:147:181:208:238:239:
+
+Even if there are no anchor points in either of parts:
+
+::
+
+    :::::::::::::::::,:::::::::108:117:125:152:186:213:243:244:
+
+
+The following table shows the correspondance between anchor point and positions in default anchor point array:
+
++--------------------------+---------------------+--------------------+
+| Anchors point            | Zero-based position | One-based position |
++==========================+=====================+====================+
+| V5UTRBeginTrimmed        | 0                   | 1                  |
++--------------------------+---------------------+--------------------+
+| V5UTREnd / L1Begin       | 1                   | 2                  |
++--------------------------+---------------------+--------------------+
+| L1End / VIntronBegin     | 2                   | 3                  |
++--------------------------+---------------------+--------------------+
+| VIntronEnd / L2Begin     | 3                   | 4                  |
++--------------------------+---------------------+--------------------+
+| L2End / FR1Begin         | 4                   | 5                  |
++--------------------------+---------------------+--------------------+
+| FR1End / CDR1Begin       | 5                   | 6                  |
++--------------------------+---------------------+--------------------+
+| CDR1End / FR2Begin       | 6                   | 7                  |
++--------------------------+---------------------+--------------------+
+| FR2End / CDR2Begin       | 7                   | 8                  |
++--------------------------+---------------------+--------------------+
+| CDR2End / FR3Begin       | 8                   | 9                  |
++--------------------------+---------------------+--------------------+
+| FR3End / CDR3Begin       | 9                   | 10                 |
++--------------------------+---------------------+--------------------+
+| VEndTrimmed              | 10                  | 11                 |
++--------------------------+---------------------+--------------------+
+| DBeginTrimmed            | 11                  | 12                 |
++--------------------------+---------------------+--------------------+
+| DEndTrimmed              | 12                  | 13                 |
++--------------------------+---------------------+--------------------+
+| JBeginTrimmed            | 13                  | 14                 |
++--------------------------+---------------------+--------------------+
+| CDR3End / FR4Begin       | 14                  | 15                 |
++--------------------------+---------------------+--------------------+
+| FR4End                   | 15                  | 16                 |
++--------------------------+---------------------+--------------------+
+| CBegin                   | 16                  | 17                 |
++--------------------------+---------------------+--------------------+
+| CExon1End                | 17                  | 18                 |
++--------------------------+---------------------+--------------------+
+
 Examples
 --------
 

diff --git a/doc/geneFeatures.rst b/doc/geneFeatures.rst
@@ -89,6 +89,12 @@ If D gene is not found in the sequence or is not present in target locus
 (e.g. TRA), ``DBeginTrimmed`` and ``DEndTrimmed`` anchor points as well
 as ``VDJunction`` and ``DJJunction`` gene features are not defined.
 
+Similar to ``...Trimmed`` anchor points in V(D)J junction there is a 
+``V5UTRBeginTrimmed`` anchor point representing left bound of alignment
+upstream start codon. This point is required because 5'UTR could have
+different length from transcript to transcript, and because library of 
+gene segments inside MiXCR does'n have information on exact 5'UTR lengths.
+
 .. _ref-featureSyntax:
 
 Gene feature syntax
@@ -119,82 +125,84 @@ it is by example:
 List of predefined gene features
 --------------------------------
 
-+----------------------------+--------------------------------------+
-| Gene Feature Name          | Gene feature decomposition           |
-+============================+======================================+
-| VGene                      | {UTR5Begin:VEnd}                     |
-+----------------------------+--------------------------------------+
-| VDJTranscript              | {UTR5Begin:L1End}+{L2Begin:FR4End}   |
-+----------------------------+--------------------------------------+
-| V5UTR                      | {UTR5Begin:UTR5End}                  |
-+----------------------------+--------------------------------------+
-| VTranscript                | {UTR5Begin:L1End}+{L2Begin:VEnd}     |
-+----------------------------+--------------------------------------+
-| Exon1                      | {L1Begin:L1End}                      |
-+----------------------------+--------------------------------------+
-| L                          | {L1Begin:L1End}+{L2Begin:L2End}      |
-+----------------------------+--------------------------------------+
-| VTranscriptWithout5UTR     | {L1Begin:L1End}+{L2Begin:VEnd}       |
-+----------------------------+--------------------------------------+
-| VLIntronL                  | {L1Begin:L2End}                      |
-+----------------------------+--------------------------------------+
-| VDJTranscriptWithout5UTR   | {L1Begin:L1End}+{L2Begin:FR4End}     |
-+----------------------------+--------------------------------------+
-| Intron                     | {VIntronBegin:VIntronEnd}            |
-+----------------------------+--------------------------------------+
-| VExon2                     | {L2Begin:VEnd}                       |
-+----------------------------+--------------------------------------+
-| Exon2                      | {L2Begin:FR4End}                     |
-+----------------------------+--------------------------------------+
-| L2                         | {L2Begin:L2End}                      |
-+----------------------------+--------------------------------------+
-| VExon2Trimmed              | {L2Begin:VEndTrimmed}                |
-+----------------------------+--------------------------------------+
-| FR1                        | {FR1Begin:FR1End}                    |
-+----------------------------+--------------------------------------+
-| VRegionTrimmed             | {FR1Begin:VEndTrimmed}               |
-+----------------------------+--------------------------------------+
-| VRegion                    | {FR1Begin:VEnd}                      |
-+----------------------------+--------------------------------------+
-| VDJRegion                  | {FR1Begin:FR4End}                    |
-+----------------------------+--------------------------------------+
-| CDR1                       | {CDR1Begin:CDR1End}                  |
-+----------------------------+--------------------------------------+
-| FR2                        | {FR2Begin:FR2End}                    |
-+----------------------------+--------------------------------------+
-| CDR2                       | {CDR2Begin:CDR2End}                  |
-+----------------------------+--------------------------------------+
-| FR3                        | {FR3Begin:FR3End}                    |
-+----------------------------+--------------------------------------+
-| VCDR3Part                  | {CDR3Begin:VEndTrimmed}              |
-+----------------------------+--------------------------------------+
-| CDR3                       | {CDR3Begin:CDR3End}                  |
-+----------------------------+--------------------------------------+
-| GermlineVCDR3Part          | {CDR3Begin:VEnd}                     |
-+----------------------------+--------------------------------------+
-| ShortCDR3                  | {CDR3Begin(3):CDR3End(-3)}           |
-+----------------------------+--------------------------------------+
-| VDJunction                 | {VEndTrimmed:DBeginTrimmed}          |
-+----------------------------+--------------------------------------+
-| VJJunction                 | {VEndTrimmed:JBeginTrimmed}          |
-+----------------------------+--------------------------------------+
-| DRegion                    | {DBegin:DEnd}                        |
-+----------------------------+--------------------------------------+
-| DCDR3Part                  | {DBeginTrimmed:DEndTrimmed}          |
-+----------------------------+--------------------------------------+
-| DJJunction                 | {DEndTrimmed:JBeginTrimmed}          |
-+----------------------------+--------------------------------------+
-| GermlineJCDR3Part          | {JBegin:CDR3End}                     |
-+----------------------------+--------------------------------------+
-| JRegion                    | {JBegin:FR4End}                      |
-+----------------------------+--------------------------------------+
-| JRegionTrimmed             | {JBeginTrimmed:FR4End}               |
-+----------------------------+--------------------------------------+
-| JCDR3Part                  | {JBeginTrimmed:CDR3End}              |
-+----------------------------+--------------------------------------+
-| FR4                        | {FR4Begin:FR4End}                    |
-+----------------------------+--------------------------------------+
-| CExon1                     | {CBegin:CExon1End}                   |
-+----------------------------+--------------------------------------+
-| CRegion                    | {CBegin:CEnd}                        |
-+----------------------------+--------------------------------------+
++---------------------------+-------------------------------------+
+| Gene Feature Name         | Gene feature decomposition          |
++===========================+=====================================+
+| V5UTRGermline             | {UTR5Begin:V5UTREnd}                |
++---------------------------+-------------------------------------+
+| VGene                     | {UTR5Begin:VEnd}                    |
++---------------------------+-------------------------------------+
+| VTranscript               | {UTR5Begin:L1End}+{L2Begin:VEnd}    |
++---------------------------+-------------------------------------+
+| VDJTranscript             | {UTR5Begin:L1End}+{L2Begin:FR4End}  |
++---------------------------+-------------------------------------+
+| V5UTR                     | {V5UTRBeginTrimmed:V5UTREnd}        |
++---------------------------+-------------------------------------+
+| VDJTranscriptWithout5UTR  | {L1Begin:L1End}+{L2Begin:FR4End}    |
++---------------------------+-------------------------------------+
+| VLIntronL                 | {L1Begin:L2End}                     |
++---------------------------+-------------------------------------+
+| L                         | {L1Begin:L1End}+{L2Begin:L2End}     |
++---------------------------+-------------------------------------+
+| VTranscriptWithout5UTR    | {L1Begin:L1End}+{L2Begin:VEnd}      |
++---------------------------+-------------------------------------+
+| Exon1                     | {L1Begin:L1End}                     |
++---------------------------+-------------------------------------+
+| Intron                    | {VIntronBegin:VIntronEnd}           |
++---------------------------+-------------------------------------+
+| Exon2                     | {L2Begin:FR4End}                    |
++---------------------------+-------------------------------------+
+| VExon2Trimmed             | {L2Begin:VEndTrimmed}               |
++---------------------------+-------------------------------------+
+| L2                        | {L2Begin:L2End}                     |
++---------------------------+-------------------------------------+
+| VExon2                    | {L2Begin:VEnd}                      |
++---------------------------+-------------------------------------+
+| VRegionTrimmed            | {FR1Begin:VEndTrimmed}              |
++---------------------------+-------------------------------------+
+| VDJRegion                 | {FR1Begin:FR4End}                   |
++---------------------------+-------------------------------------+
+| FR1                       | {FR1Begin:FR1End}                   |
++---------------------------+-------------------------------------+
+| VRegion                   | {FR1Begin:VEnd}                     |
++---------------------------+-------------------------------------+
+| CDR1                      | {CDR1Begin:CDR1End}                 |
++---------------------------+-------------------------------------+
+| FR2                       | {FR2Begin:FR2End}                   |
++---------------------------+-------------------------------------+
+| CDR2                      | {CDR2Begin:CDR2End}                 |
++---------------------------+-------------------------------------+
+| FR3                       | {FR3Begin:FR3End}                   |
++---------------------------+-------------------------------------+
+| GermlineVCDR3Part         | {CDR3Begin:VEnd}                    |
++---------------------------+-------------------------------------+
+| VCDR3Part                 | {CDR3Begin:VEndTrimmed}             |
++---------------------------+-------------------------------------+
+| CDR3                      | {CDR3Begin:CDR3End}                 |
++---------------------------+-------------------------------------+
+| ShortCDR3                 | {CDR3Begin(3):CDR3End(-3)}          |
++---------------------------+-------------------------------------+
+| VJJunction                | {VEndTrimmed:JBeginTrimmed}         |
++---------------------------+-------------------------------------+
+| VDJunction                | {VEndTrimmed:DBeginTrimmed}         |
++---------------------------+-------------------------------------+
+| DRegion                   | {DBegin:DEnd}                       |
++---------------------------+-------------------------------------+
+| DCDR3Part                 | {DBeginTrimmed:DEndTrimmed}         |
++---------------------------+-------------------------------------+
+| DJJunction                | {DEndTrimmed:JBeginTrimmed}         |
++---------------------------+-------------------------------------+
+| JRegion                   | {JBegin:FR4End}                     |
++---------------------------+-------------------------------------+
+| GermlineJCDR3Part         | {JBegin:CDR3End}                    |
++---------------------------+-------------------------------------+
+| JCDR3Part                 | {JBeginTrimmed:CDR3End}             |
++---------------------------+-------------------------------------+
+| JRegionTrimmed            | {JBeginTrimmed:FR4End}              |
++---------------------------+-------------------------------------+
+| FR4                       | {FR4Begin:FR4End}                   |
++---------------------------+-------------------------------------+
+| CRegion                   | {CBegin:CEnd}                       |
++---------------------------+-------------------------------------+
+| CExon1                    | {CBegin:CExon1End}                  |
++---------------------------+-------------------------------------+
diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsFormatter.java
@@ -86,8 +86,8 @@ public static MultiAlignmentHelper getTargetAsMultiAlignment(VDJCAlignments vdjc
     }
 
     public static final PointToDraw[] points = new PointToDraw[]{
-            pd(ReferencePoint.UTR5BeginTrimmed, "<5'UTR"),
-            pd(ReferencePoint.UTR5End, "5'UTR><L1"),
+            pd(ReferencePoint.V5UTRBeginTrimmed, "<5'UTR"),
+            pd(ReferencePoint.V5UTREnd, "5'UTR><L1"),
             pd(ReferencePoint.L1End, "L1>"),
             pd(ReferencePoint.L2Begin, "<L2"),
             pd(ReferencePoint.FR1Begin, "L2><FR1"),