Documentation for prepare_for_em

* Renamed prepare-for-rsem to prepare_for_em (make module python legal name)
* Added docs/reference file
* Altered index.rst, README and umi_tools.py to recognise the new command

Author: IanSudbery

README.rst

@@ -27,7 +27,7 @@ fastq containg UMIs +/- cell barcodes for alignment.
       barcode, for example a library barcode, is left on the read. Can
       also filter reads by quality or against a whitelist (see above)
 
-The remaining commands, ``group``, ``dedup`` and ``count``/``count_tab``, are used to
+The commands, ``group``, ``dedup`` and ``count``/``count_tab``, are used to
 identify PCR duplicates using the UMIs and perform different levels of
 analysis depending on the needs of the user. A number of different UMI
 deduplication schemes are enabled - The recommended method is
@@ -50,6 +50,10 @@ deduplication schemes are enabled - The recommended method is
 * count_tab:
    **As per count except input is a flatfile**
 
+Finally, the command ``prepare_for_em`` will take the output of ``group`` or 
+``dedup`` (after it has been name sorted or collated) and make the output
+compatible with EM tools like Salmon or RSEM. 
+
 See `QUICK_START.md <./doc/QUICK_START.md>`_ for a quick tutorial on
 the most common usage pattern.
 

doc/index.rst

@@ -61,7 +61,7 @@ for alignment.
       barcode, for example a library barcode, is left on the read. Can
       also filter reads by quality or against a whitelist (see above)
 
-The remaining commands, ``group``, ``dedup`` and
+The commands, ``group``, ``dedup`` and
 ``count``/``count_tab``, are used to identify PCR duplicates using the
 UMIs and perform different levels of analysis depending on the needs
 of the user. A number of different UMI deduplication schemes are
@@ -87,6 +87,10 @@ deduplication schemes see :doc:`the_methods`
 * count_tab:
    **As per count except input is a flatfile**
 
+Finally the command ``prepare_for_em`` takes the output of dedup or group and ensures
+that the order of reads and the matching of pairs is compatible with EM algorithms
+such as RSEM and Salmon. 
+
 .. toctree::
    :maxdepth: 1
    :caption: Commands:
@@ -97,6 +101,7 @@ deduplication schemes see :doc:`the_methods`
    dedup <reference/dedup>
    count <reference/count>
    count_tab <reference/count_tab>
+   prepare_for_em <reference/prepare_for_em>
 
 Each tool has a set of :doc:`common_options` for input/output,
 profiling and debugging.
@@ -140,7 +145,7 @@ Enter repository and run:
 
 .. code:: bash
 
-   $ python setup.py install
+   $ pip install .
 
 For more detail see :doc:`INSTALL`
 

doc/reference/prepare-for-em.rst

@@ -0,0 +1,4 @@
+Each tool has a set of :ref:`common_options` for input/output,
+profiling and debugging.
+
+.. automodule:: umi_tools.prepare_for_em

tests/umi_tools_help

@@ -4,7 +4,7 @@ For full UMI-tools documentation, see: https://umi-tools.readthedocs.io/en/lates
 umi_tools.py - Tools for UMI analyses
 =====================================
 
-:Author: Tom Smith & Ian Sudbury, CGAT
+:Author: Tom Smith & Ian Sudbery, CGAT
 :Tags: Genomics UMI
 
 There are 6 tools:
@@ -15,6 +15,7 @@ There are 6 tools:
   - dedup
   - count
   - count_tab
+  - prepare_for_em
 
 To get help on a specific tool, type:
 

umi_tools/prepare-for-rsem.py umi_tools/prepare_for_em.pyumi_tools/prepare-for-rsem.py renamed to umi_tools/prepare_for_em.py

@@ -32,13 +32,13 @@
 
 In order for this to work correctly, your input file must be sorted by read name. 
 Generally the protocol would be
-1. Align reads with your favourite aligner
+1. Align reads to the transcriptome with your favourite aligner
 2. Position sort the resulting BAM file
 3. Run `dedup` on the position sorted name file
 4. Use `samtools sort -n` or `samtools collate` to sort by read name
 5. Use `prepare_for_rsem` to create a file that has exactly one mate
    per read and that pairs are adjecent in the output.
-6. Run your downstream tools - RSEM/Salmon on the output. 
+6. Run your downstream tools - RSEM/Salmon/Kalisto on the output. 
 
 prepare-for-em specific options
 -------------------------------
@@ -47,7 +47,8 @@
 --tags=TAG[,TAG....]
 ====================
 List of SAM tags that are transfered from read1 to read2. The default
-is UG and BX
+is UG and BX, which is the numeric UMI group, and the infered true UMI
+respectively. 
 
 
 '''
@@ -169,8 +170,8 @@ def main(argv=None):
     else:
         out_name = "-"
 
-    outformat = U.determine_format(out_name, options.sam, options.out_format)
-    outbam = U.open_output_alignments(out_name, outformat, options)
+    outformat = U.determine_format(out_name, options.out_sam, options.out_format)
+    outbam = U.open_output_alignments(out_name, outformat, inbam, options)
 
     options.tags = options.tags.split(",")
 

umi_tools/umi_tools.py

@@ -2,7 +2,7 @@
 umi_tools.py - Tools for UMI analyses
 =====================================
 
-:Author: Tom Smith & Ian Sudbury, CGAT
+:Author: Tom Smith & Ian Sudbery, CGAT
 :Tags: Genomics UMI
 
 There are 6 tools:
@@ -13,6 +13,7 @@
   - dedup
   - count
   - count_tab
+  - prepare_for_em
 
 To get help on a specific tool, type:
 
@@ -46,6 +47,10 @@ def main():
 
     command = argv[1]
 
+    # substitute old name
+    if command == "prepare-for-rsem":
+        command = "prepare-for-em"
+
     try:
         module = importlib.import_module("umi_tools." + command, "umi_tools")
     except ImportError: