From 97fdefab064f63642fa3ece05b807d29b459df31 Mon Sep 17 00:00:00 2001 From: Hui Lan Date: Wed, 4 Dec 2019 19:03:19 +0800 Subject: brain: add python and R code to local repository. --- Code/configure.py | 56 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 Code/configure.py (limited to 'Code/configure.py') 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' -- cgit v1.2.1