adding script for variant data processing

scripts/loading/variant/create_NotFeature_seqs_for_align.py

@@ -0,0 +1,53 @@
+# loop through each fasta seq row from all 12 strains and create a file for each feature if there are two or more strains have the seq for the given feature
+
+inDir = "data/not_feature_fasta/"
+outDir = "data/not_feature_seq/"
+
+ref_strain_file = inDir + "not_feature_S288C.fsa"
+
+alt_strains = [ "W303", "FL100", "CEN.PK", "Sigma1278b", "SK1", "D273-10B",
+                "X2180-1A", "Y55", "JK9-3d", "SEY6210", "RM11-1a" ]
+
+altSeqID2seq = {}
+for strain in alt_strains:
+    file = inDir + "not_feature_" + strain + ".fsa"
+    f = open(file)
+    seqID = None
+    for line in f:
+        if line.startswith(">"):
+            seqID = line.split(' ')[0]
+        else:
+            altSeqID2seq[seqID] = line
+    f.close()
+
+f = open(ref_strain_file)
+
+seqID = None
+
+for line in f:
+
+    if line.startswith(">"):
+
+        seqID = line.split(' ')[0]
+
+    else:
+
+        seq = line
+
+        count = 0
+        for strain in alt_strains:
+            altSeqID = seqID.replace('S288C', strain)
+            if altSeqID in altSeqID2seq:
+                count = count + 1
+
+        if count > 0:
+            outfile = outDir + seqID.replace("|S288C", "").replace(">", "").replace("|", "_") + ".seq"
+            fw = open(outfile, "w")
+            fw.write(seqID.replace("|", "_") + "\n")
+            fw.write(seq)
+            for strain in alt_strains:
+                altSeqID = seqID.replace('S288C', strain)
+                if altSeqID in altSeqID2seq:
+                    fw.write(altSeqID.replace("|", "_") + "\n")
+                    fw.write(altSeqID2seq[altSeqID])
+            fw.close()