Added some more stuff to facilitate table formatting
modified how address is handled
modified to generate R plot automatically
modified to allow piped input from STDIN
modified to also write to STDOUT
added functions add_coding, ref_coding, add_orthologs and non_redundant; modified add_seqs

add_coding parses a BED file from TransDecoder and adds coordinates of coding seqs to DB

ref_coding simply copies reference seqIDs to geneIDs and adds start and end of seq as coding coordinates

add_orthologs parses output of orthoMCL and adds the info to the DB

non_redundant updates the non_redundant field of OrthoGroups to 1 for all sequences in the output of PhyloTreePruner
modified seq_clusters to work on individual clusters, added get_clusters

seq_clusters will now output sequences belonging to the specified cluster. This can be looped with a shell script:

for f in {0..6000}
do
  GetData.py -f seq_clusters -c $i
done

I also added get_clusters which gets a list of ALL clusters present in the specified species
added line to cleanup R script
modified seq_clusters to "_" to "|" as the delimiter between species id and seq id
modified seq_clusters to trim sequences to coding portions and revcom if necessary

I also modified the name from seqID to geneID
first commit (downloaded from http://pc16141.mncn.csic.es/cgi-bin/translatorx_vLocal.pl)
modified to create outfiles (and logfile) based on name of infile
Fixed the coordinates for BED file parsing

the coodinates are for the gene, not the CDS. The gene is inferred by TransDecoder to be
the full length of the transcript. I am now using the thickStart and thickEnd coordinates
instead, which correspond to the CDS.

I also corrected the start coordinates so they correspond to standard numbering
fixed bug in parsing of 3prime_partial features
Added a function to add genbank data to a database for phylogenetics

I also added an option to specify a different DB from SelaginellaGenomics, leaving that as the default
added function to get all sequences from a specified locus

I also added an option to specify the name of the database, because this function is
designed to work with the BegoniaPhylogenetics database.

I also added an option to specify an outfile rather than printing the output to STDOUT
-this is useful in cases where you want to loop through a lot of input values using a
shell script, but only want to create an outfile when data is returned from the DB
-currently, this option has only been added to the seq_clusters function, but it is
trivial to add it to others
fixed error with reverse-complemented sequences

Sequences are retrieved from the DB as strings so it is not possible to reverse-complement
them without converting them to sequence objects first. That step has not been added
moved filehandle opening into seq_clusters function

This was necessary because if it's opened before checking for BLUELEAF sequences, it
defeats the purpose of using a filehandle rather than printing to STDOUT
first commit