README.md in bio-polyploid-tools-0.7.0 vs README.md in bio-polyploid-tools-0.7.1
- old
+ new
@@ -19,27 +19,76 @@
#PolyMarker
To run poolymerker with the CSS wheat contigs, you need to unzip the
-(reference file)[ftp://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz
-].
+[reference file](ftp://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz
+).
```sh
polymarker.rb --contigs Triticum_aestivum.IWGSC2.25.dna.genome.fa --marker_list snp_list.csv --output output_folder
```
-The snp_list file must follow the convention
-<ID>,<Chromosome>,<SEQUENCE>
+The ```snp_list``` file must follow the convention
+```<ID>,<Chromosome>,<SEQUENCE>```
with the SNP inside the sequence in the format [A/T]. As a reference, look at test/data/short_primer_design_test.csv
If you want to use the web interface, visit the [PolyMarker webservice at TGAC](http://polymarker.tgac.ac.uk)
+The available command line arguments are:
+
+```
+Usage: polymarker.rb [options]
+ -c, --contigs FILE File with contigs to use as database
+ -m, --marker_list FILE File with the list of markers to search from
+ -g, --genomes_count INT Number of genomes (default 3, for hexaploid)
+ -s, --snp_list FILE File with the list of snps to search from, requires --reference to get the sequence using a position
+ -t, --mutant_list FILE File with the list of positions with mutation and the mutation line.
+ requires --reference to get the sequence using a position
+ -r, --reference FILE Fasta file with the sequence for the markers (to complement --snp_list)
+ -o, --output FOLDER Output folder
+ -e, --exonerate_model MODEL Model to be used in exonerate to search for the contigs
+ -a, --arm_selection arm_selection_embl|arm_selection_morex|arm_selection_first_two
+ Function to decide the chromome arm
+ -p, --primer_3_preferences FILE file with preferences to be sent to primer3
+ -v, --variation_free_region INT If present, avoid generating the common primer if there are homoeologous SNPs within the specified distance (not tested)
+ -x, --extract_found_contigs If present, save in a separate file the contigs with matches. Useful to debug.
+ -P, --primers_to_order If present, saves a file named primers_to_order which contains the KASP tails
+```
+
+###Custom reference sequences.
+By default, the contigs and pseudomolecules from [ensembl](ftp://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz
+) are used. However, it is possible to use a custom reference. To define the chromosome where each contig belongs the argument ```arm_selection``` is used. The defailt uses ids like: ```IWGSC_CSS_1AL_scaff_110```, where the third field, separated by underscores is used. A simple way to add costum references is to rename the fasta file to follow that convention. Another way is to use the option ```--arm_selection arm_selection_first_two```, where only the first two characters in each contig is used as identifier, useful when pseudomolecules are named after the chromosomes (ie: ">1A" in the fasta file).
+
+If your contigs follow a different convention, in ```polymarker.rb``` it is possible to define new parsers, by adding at the begining, with the rest of the parsers a new lambda like:
+
+```rb
+arm_selection_functions[:arm_selection_embl] = lambda do | contig_name|
+ arr = contig_name.split('_')
+ ret = "U"
+ ret = arr[2][0,2] if arr.size >= 3
+ ret = "3B" if arr.size == 2 and arr[0] == "v443"
+ ret = arr[0][0,2] if arr.size == 1
+ return ret
+end
+```
+
+The function should return a 2 character string, when the first is the chromosome number and the second the chromosome group. The symbol in the hash is the name to be used in the argument ```--arm_selection```. If you want your parser to be added to the distribution, feel free to fork and make a pull request.
+
+
+
##Release Notes
+###0.7.1
+* BUGFIX: Now the parser for ```arm_selection_embl``` works with the mixture of contigs and pseudomolecules
+* DOC: Added documentation on how to use custom references.
+
+###0.7.0
+* Added flag ```gebines_count``` for number of genomes, to be used on tetraploids, etc.
+
###0.6.1
* polymarker.rb now validates that all the files exist.
* BUGFIX: A reference was required even when it was not used to generate contigs.
@@ -47,13 +96,13 @@
#Notes
* If the SNP is in a gap in the alignment to the chromosomes, it is ignored.
-BUG: Blocks with NNNs are picked and treated as semi-specific.
-BUG: If the name of the reference have space, the ID is not chopped. ">gene_1 (G12A)" shouls be treated as ">gene_1".
-TODO: Add a parameter file to configure the alignments.
-TODO: Produce primers for products of different sizes
+* BUG: Blocks with NNNs are picked and treated as semi-specific.
+* BUG: If the name of the reference have space, the ID is not chopped. ">gene_1 (G12A)" shouls be treated as ">gene_1".
+* TODO: Add a parameter file to configure the alignments.
+* TODO: Produce primers for products of different sizes. This can probably be done with the primer_3_preferences option, but hasn't been tested.