no message

BRIC-seq_Tutorial/extract_gene_symbol_type_from_gtf.py

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+#!/usr/bin/env python2
+
+from __future__ import print_function
+import sys
+
+input_file = open(sys.argv[1], 'r')
+output_file = open(sys.argv[2], 'w')
+tmp_file = open('anno_tmp.txt', 'w')
+
+ref_dict = {}
+# gene_id | gene_name | Akimitsu_anno | Gencode_anno
+
+for line in input_file:
+    line = line.rstrip()
+    data = line.split("\t")
+    if line.startswith('#'):
+        continue
+    status = data[2]
+    gene_infor = data[8].split('; ')
+
+    if data[1] == 'FAMTOM5':
+        gene_name = ''
+        chrom = data[0]
+        st = data[3]
+        ed = data[4]
+        strand = data[6]
+        chrom_infor = chrom + ':' + st + '-' + ed + ',' + strand
+        for x in gene_infor:
+            if x.startswith('gene_name'):
+                x = x.replace('gene_name "', '')
+                x = x.replace('"', '')
+                x = x.replace(';', '')
+                gene_name = x
+                print(gene_name, "NA", 'FANTOM5_eRNA', 'NA',chrom_infor, sep="\t", end="\n", file=output_file)
+                continue
+    elif data[1] == 'AkimitsuLab':
+        gene_name = ''
+        chrom = data[0]
+        st = data[3]
+        ed = data[4]
+        strand = data[6]
+        chrom_infor = chrom + ':' + st + '-' + ed + ',' + strand
+        for x in gene_infor:
+            if x.startswith('gene_name'):
+                x = x.replace('gene_name "', '')
+                x = x.replace('"', '')
+                x = x.replace(';', '')
+                gene_name = x
+                if gene_name.startswith('ERNA'):
+                    print(gene_name, "NA", 'Akimitsu_eRNA', 'NA',chrom_infor, sep="\t", end="\n", file=output_file)
+                    continue
+                elif gene_name.startswith('PROT'):
+                    print(gene_name, "NA", 'Akimitsu_PROMPT', 'NA',chrom_infor, sep="\t", end="\n", file=output_file)
+                    continue
+
+    if status == 'gene':
+        gene_type = ''
+        gene_name = ''
+        gene_id = ''
+        chrom = data[0]
+        st = data[3]
+        ed = data[4]
+        strand = data[6]
+        chrom_infor = chrom + ':' + st + '-' + ed + ',' + strand
+        for x in gene_infor:
+            if x.startswith('gene_type'):
+                x = x.replace('gene_type "', '')
+                x = x.replace('"', '')
+                gene_type = x
+            elif x.startswith('gene_name'):
+                x = x.replace('gene_name "', '')
+                x = x.replace('"', '')
+                gene_name = x
+            elif x.startswith('gene_id'):
+                x = x.replace('gene_id "', '')
+                x = x.replace('"', '')
+                gene_id = x
+        ref_dict[gene_id] = [gene_type, gene_name, gene_id, chrom_infor]
+
+mRNA_list = [
+"protein_coding"
+]
+
+lncRNA_list = [
+"3prime_overlapping_ncrna",
+"antisense",
+"lincRNA",
+"misc_RNA",
+"sense_intronic",
+"sense_overlapping"
+]
+
+pseudogene_list = [
+"IG_C_pseudogene",
+"IG_J_pseudogene",
+"IG_V_pseudogene",
+"polymorphic_pseudogene",
+"processed_pseudogene",
+"pseudogene",
+"TR_J_pseudogene",
+"TR_V_pseudogene",
+"transcribed_processed_pseudogene",
+"transcribed_unprocessed_pseudogene",
+"translated_processed_pseudogene",
+"unitary_pseudogene",
+"unprocessed_pseudogene"
+]
+
+processed_transcript_list = [
+"processed_transcript"
+]
+
+print('# gene_id | gene_symbol | Akimitsu_lab_type | Gencode_gene_type | chrom_infor', end="\n", file=output_file)
+
+mRNA_gene_name_dict = {}
+
+for key in ref_dict.keys():
+    gene_infor = ref_dict[key]
+    gene_type = gene_infor[0]
+    gene_name = gene_infor[1]
+    gene_id = gene_infor[2]
+    chrom_infor = gene_infor[3]
+    if gene_type in mRNA_list:
+        print(gene_id, gene_name, "mRNA", gene_type,chrom_infor, sep="\t", end="\n", file=output_file)
+        mRNA_gene_name_dict[gene_name] = 1
+    elif gene_type in lncRNA_list:
+        print(gene_id, gene_name, "lncRNA", gene_type,chrom_infor, sep="\t", end="\n", file=output_file)
+    elif gene_type in pseudogene_list:
+        print(gene_id, gene_name, "pseudogene", gene_type,chrom_infor, sep="\t", end="\n", file=output_file)
+    elif gene_type in processed_transcript_list:
+        print(gene_id, gene_name, "pending", gene_type,chrom_infor, sep="\t", end="\n", file=tmp_file)
+    else:
+        print(gene_id, gene_name, "others", gene_type,chrom_infor, sep="\t", end="\n", file=output_file)
+
+tmp_file.close()
+
+for line in open("anno_tmp.txt", 'r'):
+    line = line.rstrip()
+    data = line.split("\t")
+    gene_name = data[1]
+    if gene_name in mRNA_gene_name_dict:
+        print("checked" + gene_name)
+        print(data[0], data[1], "black", data[3], data[4], sep="\t", end="\n", file=output_file)
+        continue
+    print(data[0], data[1], "lncRNA", data[3], data[4], sep="\t", end="\n", file=output_file)

Strand-specific_RNA-seq_Tutorial/RNA-seq_test_run.sh

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+#!/bin/bash
+
+for file in *.fastq
+do
+    qsub ./RNA-seq_strand-specific_single-end_1_mapping.sh ${file}
+done