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dbolotin committed Oct 6, 2015
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2 changes: 2 additions & 0 deletions .gitignore
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19 changes: 19 additions & 0 deletions CHANGELOG
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MiXCR 1.6 ( 6 Oct 2015)
========================

-- 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`)
-- 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
-- MiXCR execution script now passes java-specific options directly to JVM (e.g. you can execute
`mixcr -Xmx2g align ...`)
-- Added `V5UTRBeginTrimmed` anchor point, `V5UTR` gene feature renamed to `V5UTRGermline`, trimmed
`V5UTR` gene feature added
-- Added `--filter-out-of-frames` and `--filter-stops` options in `exportClones`
-- minor: some column names in output tab-delimited files slightly changed
-- minor: NPE in exportAlignmentsPretty fixed
-- minor: New anchor poins added to exportAlignmentsPretty output


MiXCR 1.5 (11 Sep 2015)
========================

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7 changes: 7 additions & 0 deletions README.md
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Detailed documentation can be found at https://mixcr.readthedocs.org/.

---

*Please cite:*

Bolotin, Dmitriy A., Stanislav Poslavsky, Igor Mitrophanov, Mikhail Shugay, Ilgar Z. Mamedov, Ekaterina V. Putintseva, and Dmitriy M. Chudakov. "MiXCR: software for comprehensive adaptive immunity profiling." *Nature methods* 12, no. 5 (**2015**): 380-381.
82 changes: 81 additions & 1 deletion doc/export.rst
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Expand Up @@ -84,6 +84,9 @@ The list of command line parameters for both ``exportAlignments`` and
+---------------------+-------------------------------------------------------------------+
| -pf, --presetFile | load file with a list of fields to export |
+---------------------+-------------------------------------------------------------------+
| -s, --no-spaces | output short versions of column headers which facilitates analysis|
| | with Pandas, R/DataFrames or other data tables processing library |
+---------------------+-------------------------------------------------------------------+

Available fields
----------------
Expand Down Expand Up @@ -143,6 +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:

Expand Down Expand Up @@ -180,6 +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 one of the 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
--------

Expand Down Expand Up @@ -211,7 +291,7 @@ MiXCR allows to export resulting alignments after :ref:`align <ref-align>`
step as a pretty formatted text for manual analysis of produced
alignments and structure of library to facilitate optimization of
analysis parameters and libraray preparation protocol. To export pretty
formatted alignments use ``exportAlignmebtsPretty`` command:
formatted alignments use ``exportAlignmentsPretty`` command:

::

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166 changes: 87 additions & 79 deletions doc/geneFeatures.rst
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Expand Up @@ -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
Expand Down Expand Up @@ -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} |
+---------------------------+-------------------------------------+
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