script to prep EAGER tsv input from sqlite

scripts/sqlite_EAGER_tsv.py

@@ -0,0 +1,193 @@
+#!/usr/bin/env python3
+"""
+@author: Katherine Eaton
+
+sqlite_sra_parse.py
+
+./sqlite_sra_parse.py \
+  --database ../results/ncbimeta_db/update/latest/output/database/yersinia_pestis_db.sqlite \
+  --query "SELECT SRASampleName,SRARunAccession, SRALibraryLayout,SRAFileURL From Master WHERE ( BioSampleComment LIKE '%KEEP%')" \
+  --organism "Yersinia pestis" \
+  --output "metadata.tsv"
+"""
+
+# This program should only be called from the command-line
+if __name__ != "__main__": quit()
+
+#-----------------------------------------------------------------------#
+#                         Modules and Packages                          #
+#-----------------------------------------------------------------------#
+import argparse                         # Command-line argument parsing
+import sqlite3                          # Database storage and queries
+import sys                               # Filepath operations
+
+#-----------------------------------------------------------------------#
+#                            Argument Parsing                           #
+#-----------------------------------------------------------------------#
+
+parser = argparse.ArgumentParser(description='Short description goes here.',
+                                 add_help=True)
+
+# Argument groups for the program
+
+parser.add_argument('--database',
+                    help = 'Path to the NCBImeta sqlite database.',
+                    action = 'store',
+                    dest = 'dbPath',
+                    required = True)
+
+parser.add_argument('--query',
+                    help = 'SQL query command.',
+                    action = 'store',
+                    dest = 'sqlQuery',
+                    required = True)
+
+parser.add_argument('--organism',
+                    help = 'Organism name for EAGER (Genus species).',
+                    action = 'store',
+                    dest = 'orgName',
+                    required = True)
+
+parser.add_argument('--output',
+                    help = 'Output tsv file for EAGER.',
+                    action = 'store',
+                    dest = 'outPath',
+                    required = True)
+
+# Retrieve user parameters
+args = vars(parser.parse_args())
+
+db_path = args['dbPath']
+sql_query = args['sqlQuery']
+org_name = args['orgName']
+out_path = args['outPath']
+
+#------------------------------------------------------------------------------#
+#                            Error Catching                                    #
+#------------------------------------------------------------------------------#
+
+# Check if DATABASE file exists
+try:
+    conn = sqlite3.connect(db_path)
+    cur = conn.cursor()
+except IOError:
+    print('An error occurred while trying to open ', db_path)
+    sys.exit(1)
+
+# Open the output file
+out_file = open(out_path, 'w')
+
+#------------------------------------------------------------------------------#
+#                              Default Variables                               #
+#------------------------------------------------------------------------------#
+# EAGER tsv input column names
+EAGER_HEADER="Sample_Name\tLibrary_ID\tLane\tSeqType\tOrganism\tStrandedness\tUDG_Treatment\tR1\tR2\tBAM\tGroup\tPopulations\tAge";
+
+# Indices for retrieved values
+BIOSAMPLE_ACC_IND = 0
+SRA_ACC_IND = 1
+LIBRARY_LAYOUT_IND = 2
+FTP_URL_IND = 3
+
+# By default assume basic or NA values for these columns
+LANE="1"
+BAM="NA"
+GROUP="NA"
+POPULATIONS="NA"
+AGE="NA"
+
+# By default assume double stranded for now
+STRANDEDNESS="DOUBLE"
+
+# Separator for record values
+DB_SEP = ";"
+
+#------------------------------------------------------------------------------#
+#                                Processing                                    #
+#------------------------------------------------------------------------------#
+
+# Select the desired records
+cur.execute(sql_query)
+
+# 0 if not found, 1 if found
+record_exists = cur.fetchall()
+
+# Print the default EAGER header
+out_file.write(EAGER_HEADER + "\n")
+
+# If the record_exists, skip the whole next part (ie. "continue" to next record)
+for record in record_exists:
+    # Biosample Accession
+    biosample_acc = record[BIOSAMPLE_ACC_IND]
+    # SRA Run Accession
+    sra_acc = record[SRA_ACC_IND]
+    sra_acc_split = sra_acc.split(DB_SEP)
+
+    # Get FTP links, relying on them being in order
+    ftp_url = record[FTP_URL_IND]
+    ftp_url_split = ftp_url.split(DB_SEP)
+
+    # Remove URLs that are not from the FTP site
+    for url_val in ftp_url_split:
+        if not url_val.startswith("http://ftp"):
+            ftp_url_split.remove(url_val)
+
+    # Library Layout, SINGLE or PAIRED, convert to EAGER SE or PE
+    library_layout = record[LIBRARY_LAYOUT_IND]
+    # Initialize default path to NA
+    R1_path = "NA"
+    R2_path = "NA"
+    # Parse FTP url differently based on SINGLE or PAIRED
+    if library_layout == "SINGLE":
+        library_layout = "SE"
+        ftp_i = 0
+        sra_i = 0
+
+        while ftp_i < len(ftp_url_split):
+            sra_acc_val = sra_acc_split[sra_i]
+            R1_path = ftp_url_split[ftp_i]
+            out_file.write(biosample_acc + "\t" +
+                  sra_acc_val + "\t" +
+                  LANE + "\t" +
+                  library_layout + "\t" +
+                  org_name + "\t" +
+                  R1_path + "\t" +
+                  R2_path + "\t" +
+                  BAM + "\t" +
+                  GROUP + "\t" +
+                  POPULATIONS + "\t" +
+                  AGE + "\n")
+            ftp_i += 1
+            sra_i += 1
+
+
+
+    elif library_layout == "PAIRED":
+        library_layout = "PE"
+        ftp_i = 0
+        sra_i = 0
+        while ftp_i < len(ftp_url_split):
+            sra_acc_val = sra_acc_split[sra_i]
+            R1_path = ftp_url_split[ftp_i]
+            R2_path = ftp_url_split[ftp_i+1]
+            out_file.write(biosample_acc + "\t" +
+                  sra_acc_val + "\t" +
+                  LANE + "\t" +
+                  library_layout + "\t" +
+                  org_name + "\t" +
+                  R1_path + "\t" +
+                  R2_path + "\t" + 
+                  BAM + "\t" +
+                  GROUP + "\t" +
+                  POPULATIONS + "\t" +
+                  AGE + "\n")
+            ftp_i+=2
+            sra_i+=1
+
+
+#------------------------------------------------------------------------------#
+#                            Clean Up                                          #
+#------------------------------------------------------------------------------#
+conn.commit()
+cur.close()
+out_file.close()