add helper function help_concatenate-core-alignments.py

scripts/help_concatenate-core-alignments.py

@@ -0,0 +1,31 @@
+import os, json, gzip
+import argparse
+from Bio import SeqIO
+from collections import defaultdict
+from sf_miscellaneous import write_in_fa
+
+parser = argparse.ArgumentParser(description='run this script in the ./scripts/ folder: concatenate all core gene alignments based on the core_geneList.txt file in the folder ./geneCluster/ ',\
+         usage=' python %(prog)s'+'  -in ../data/TestSet/ -out /yourPath/concatenated_core_gene_alignments.fa')
+parser.add_argument('-in',  '--input_filepath',  type = str, required=True, help='')
+parser.add_argument('-out', '--output_filepath', type = str, required=True, help='')
+params = parser.parse_args()
+input_filepath=params.input_filepath
+output_filepath=params.output_filepath
+
+def concatenate_core_gene_alignments(input_path, output_path):
+    core_genes_dt=defaultdict(str)
+    with open(input_path+'/geneCluster/core_geneList.txt') as core_list:
+    # all core gene alignments in FASTA files
+        for gene in core_list:
+            gene_path= input_path+'/vis/geneCluster/'+gene.rstrip()+'.gz'
+            with gzip.open(gene_path, 'rb') as zip_file:
+                for record in SeqIO.parse(zip_file, "fasta"):
+                    #NC_018495-CM9_RS00390-1-hypothetical_protein
+                    accession=record.id.split('-')[0]
+                    core_genes_dt[accession]= '%s%s'%(core_genes_dt[accession], record.seq)
+
+    with open(output_path,'wb') as output_file:
+        for gene_id, gene_seq in core_genes_dt.iteritems():
+            write_in_fa(output_file, gene_id, gene_seq)
+
+concatenate_core_gene_alignments(input_filepath, output_filepath)