Pseudopipe Copyright 2016 Mark B. Gerstein Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. === === === === This archive consists of a standalone version of pseudopipe pipeline and a simple try-out data. Since the pipeline was originally designed and automated to work with ensembl data, so some manual settings are required to run it with other input data. === There are three folders within a parent directory "pgenes" after extraction of the archive: === - pseudopipe: which contains pipeline code; - ppipe_input: which contains input data; - ppipe_output: which contains output data. === Input data: === You may create a separate folder within the ppipe_input (and ppipe_output) for each species. There need to be three folders for each species genomic input data, - dna: contains a file named dna_rm.fa, which is entire repeat masked dna from that species, and a list file for all unmasked dna divided into different chromosomes in FASTA format; - pep: contains a FASTA file for all the proteins in the species; - mysql: contains a list of files named as "chr1_exLocs", "chr2_exLocs", etc. to specify exons coordinates, one for each chromosome. Only thing matters for these files are their third and fourth columns, which should be start and end coordinates of exons. === Environment setting: === You'll need python, blast and tfasty to run the pipeline. Their paths should be indicated at the end of /pseudopipe/bin/env.sh === Run the pipeline === First go to the folder pseudopipe/bin, and run with command line in the form of: ./pseudopipe.sh [output dir] [masked dna dir] [input dna dir] [input pep dir] [exon dir] 0. An example using the try-out data is as follow: ./pseudopipe.sh ~/pgenes/ppipe_output/caenorhabditis_elegans_62_220a ~/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa ~/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa ~/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa ~/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chr%s_exLocs 0 (This command line assumes you extract the archive in your home directory, i.e., "~/". Please note that the paths in the command line need to be absolute, and chromosome and exon files are specified with wild card "%s".) The blast step is already included in the pipeline. === Output: === The output can be found at ppipe_output/caenorhabditis_elegans_62_220a/pgenes/ppipe_output_pgenes.txt, given the above command line. === Run time === On a single laptop (2.6GHz, 4GB RAM): The most time consuming step is tblastn. It may take around one day to finish an entire genome in a comparable size of C. elegans. The following steps will finish in a few hours. We've implemented the pipeline to run parallel in cluster machines. However, the pipeline I sent can only run on a single machine. The parallel implementation is currently hard-coded to our local settings.