brain: add python and R code to local repository.

1 files changed, 56 insertions, 0 deletions

diff --git a/Code/configure.py b/Code/configure.py
new file mode 100644
index 0000000..c740e98
--- /dev/null
+++ b/Code/configure.py
@@ -0,0 +1,56 @@
+# From get_TPM_by_salmon.py

+SALMON          = '/home/lanhui/brain/Salmon/Salmon-0.7.2_linux_x86_64/bin/salmon' # salmon software path

+SALMON_INDEX    = '/home/lanhui/brain/Salmon/salmon_index'

+TRANSCRIPTOME   = '/home/lanhui/brain/Salmon/Arabidopsis_thaliana.TAIR10.cdna.all.fa'

+SALMON_MAP_RESULT_DIR = '../Data/temp/salmon_map_result'

+KMER            = 31

+

+# From download_and_map.py

+DAILY_MAP_NUMBER = 5   # download this many samples each time.  I have tested the values of 3, 4, 5, 8.

+MIN_FASTQ_FILE_SIZE = 200000000    # in bytes, approximately 200MB

+RNA_SEQ_INFO_FILE = '../Data/information/rnaseq_info_database.json'  # some data downloaded from ENA are not RNA-seq (they are ChIP-seq). Use this file to tell whether the file is RNA-seq

+DOWNLOADED_SRA_ID_LOG_FILE = '../Data/log/download_log.txt' # a list of downloaded SRA IDs

+IGNORED_SRA_ID_LOG_FILE = '../Data/log/download_log_small_sized_ids.txt'  # store SRA IDs with small file size.

+MAPPED_RDATA_DIR = '../Data/R/Mapped/public'          # mapped RNA-seq (file names ended with _quant.txt) go here

+RAW_RDATA_DIR    = '../Data/R/Raw'                       # downloaded files go here

+

+

+# From update_network.py

+# Don'T change the following paths and names

+HISTORY_DIR       = '../Data/history/edges/many_targets' # each edge file contains edges for many targets

+HISTORY_DIR2      = '../Data/history/edges/one_target'   # edges.txt.* files are here, all edge files have the name edges.txt.*, the leading string 'edges.txt' must be present.

+FILE_TIMESTAMP    = '../Data/log/file_timestamp.txt'     # record last modified time of several important files

+SAMPLE_SIZE_FILE  = '../Data/log/total.samples.txt'      # each line contains a date and the number of samples on and after that date

+TEMP_DIR          = '../Data/temp'

+

+PARAMETER_FOR_BUILDCMATRIX = '../Data/parameter/parameter_for_buildCmatrix.txt'

+PARAMETER_FOR_BUILDRMATRIX = '../Data/parameter/parameter_for_buildRmatrix.txt'

+PARAMETER_FOR_NET          = '../Data/parameter/parameter_for_net.txt'

+PARAMETER_FOR_NET_TRAVADB_STRESS      = '../Data/parameter/parameter_for_net_travadb_stress.txt'

+PARAMETER_FOR_NET_TRAVADB_MAP         = '../Data/parameter/parameter_for_net_travadb_map.txt'

+PARAMETER_FOR_NET_MILD_DROUGHT        = '../Data/parameter/parameter_for_net_mild_drought.txt'

+PARAMETER_FOR_NET_WIGGELAB_DIURNAL    = '../Data/parameter/parameter_for_net_wiggelab_diurnal.txt'

+

+BINDING_FILE               = '../Data/history/bind/binding.txt'

+TPM_FILE                   = '../Data/history/expr/TPM.txt' # gene expression data

+

+PARAMETER_FOR_BUILDRMATRIX_RENEW_INTERVAL = 1 # check every 28 days for updating TPM.txt

+MIN_RNA_SEQ_INCREASE = 2 # minimum RNA-seq experiments needed when updating parameter_for_buildRmatrix.txt

+UPDATE_NETWORK_LOG_FILE  = '../Data/log/update.network.log.txt' # network update log. We should check this file from time to time.

+NEW_OR_UPDATED_CHIP_FILE = '../Data/log/new.or.updated.chip.file.txt'

+

+RNA_SEQ_INFO_DATABASE   = '../Data/information/rnaseq_info_database.txt' # same as RNA_SEQ_INFO_FILE

+RNA_SEQ_INFO_DATABASE_JSON   = '../Data/information/rnaseq_info_database.json'

+

+GENE_ID_FIRST_TWO_LETTERS = 'AT'

+MEMORY_STRENGTH = 365 # strength of memory, larger value means better memory

+

+#

+MAPPED_CDATA_DIR = '../Data/C/Mapped' # mapped ChIp-seq data

+

+# Used in merge_edges.py

+EDGE_POOL_DIR = '../Data/history/edge_pool'

+MERGED_EDGE_FILE = '../Data/temp/edges.txt'

+

+

+TARGET_TF_FILE = '../Data/information/target_tf.txt'