diff --git a/README.md b/README.md
index 3c0ea33db568787880606f9f6015fb29b58c829a..182330ab8e7971e7554a61e25ef684ada5a880e6 100644
--- a/README.md
+++ b/README.md
@@ -31,10 +31,10 @@ package manager. We recommend that you install
For improved reproducibility and reusability of the workflow, as well as an
easy means to run it on a high performance computing (HPC) cluster managed,
-e.g., by [Slurm][slurm], almost all steps of the workflow run in their own
-container. As a consequence, running this workflow has very few individual
-dependencies. It does, however, require that the container engine
-[Singularity][singularity] is installed.
+e.g., by [Slurm][slurm], all steps of the workflow run in their own container.
+As a consequence, running this workflow has very few individual dependencies. It
+does, however, require that the container engine [Singularity][singularity] is
+installed.
Create and activate the environment with necessary dependencies with conda:
diff --git a/scripts/split_file_by_colum_value.sh b/scripts/split_file_by_colum_value.sh
deleted file mode 100755
index 62169059c0a052fec957bbd092cb7ce42b6a2906..0000000000000000000000000000000000000000
--- a/scripts/split_file_by_colum_value.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/bin/bash
-
-# Setting to strict mode
-set -euo pipefail
-IFS=$'\n\t'
-
-#### FUNCTIONS
-
-usage()
-{
- echo "usage: split_file_by_colum_value.sh [[[-f file] [-c column] [-s separator]] | [-h]]"
-}
-
-
-
-#### MAIN
-# Test whether all required inputs are present
-if [[ $1 == -h ]] || [[ $# != 6 ]]
-then
- usage
- exit
-fi
-
-# Get parameters
-while [ $# -gt 0 ]; do
- case $1 in
- -f | --file ) shift
- filename=$1
- ;;
- -c | --column ) shift
- column=$1
- ;;
- -s | --separator ) shift
- separator=$1
- ;;
- -h | --help ) usage
- exit
- ;;
- * ) usage
- exit 1
- esac
- shift
-done
-
-printf "\nFile splited by colum %i values.\n" \
- ${column}\
-
-# Split file by values in requested column
-awk -v col="${column}" -v sep="${separator}" -F'$sep' '{print > $col".txt"}' ${filename}
-
-printf "\nDONE!\n"
diff --git a/scripts/validation_fasta.py b/scripts/validation_fasta.py
deleted file mode 100755
index f39059e37e2f0c1c119ed7205742d368a6185cab..0000000000000000000000000000000000000000
--- a/scripts/validation_fasta.py
+++ /dev/null
@@ -1,170 +0,0 @@
-#!/usr/bin/env python
-import sys
-import re
-import gzip
-from argparse import ArgumentParser, RawTextHelpFormatter
-
-
-### Created: Mar 5, 2019
-### Author: Paula Iborra
-### Company: Zavolan Group, Biozentrum, University of Basel
-
-
-### ARGUMENTS ###
-
-parser = ArgumentParser(
- description="Script to filter FASTA files"
- )
-parser.add_argument(
- '-v','--version',
- action='version',
- version='%(prog)s 1.0',
- help="Show program's version number and exit"
- )
-parser.add_argument(
- '--trim',
- help="Character's used to trim the ID. Remove anything that follows the character's. Write \\ infront of \'.\' and \'-\'(i.e trim=\"$\\.\\-|_\"). Default: first white space",
- type=str,
- nargs='?',
- default=""
- )
-parser.add_argument(
- '--idlist',
- help="Generate text file with the sequences IDs. One ID per line."
- )
-parser.add_argument(
- '-f','--filter',
- help="Input ID list. Filter IDs and sequences from FASTA file with the mode selected. Filter file must contain ONE ID per line",
- )
-parser.add_argument(
- '-m', '--mode',
- help="Type of filtering fasta file: keep (k) or discard (d) IDs contained in the ID list file.",
- choices=('k', 'd')
- )
-parser.add_argument(
- '-r','--remove',
- help="Remove sequences from FASTA file longer than specified length.",
- type=int
- )
-parser.add_argument(
- '-i','--input',
- required=True,
- help="Input FASTA file",
- type=str
- )
-parser.add_argument(
- '-o','--output',
- help="Output FASTA file"
- )
-
-args = parser.parse_args()
-
-if args.filter and not args.mode:
- sys.exit("ERROR! Mode argument required when using filter option. (--mode, -m). See --help option.")
-
-### PARSE FASTA FILE ###
-
-class Seq:
- def __init__(self):
- self.id=""
- def __init__(self):
- self.seq=""
- def __init__(self):
- self.features=""
-
-# open files
-if args.input.endswith('.gz'):
- f = gzip.open(args.input, 'rt')
-else:
- f = open(args.input)
-
-record=[] #list of records
-nrec=-1
-inseq=0
-
-# parse fasta file
-sys.stdout.write("Parsing FASTA file...")
-for line in f:
- if re.match(r'^>' , line):
- nrec+=1
- record.append(Seq())
-
- # define id of the record
- if not args.trim:
- mobj=re.match(r'^>(\S*)(.*)', line)
- else:
- mobj=re.match(r'^>([^%s]*)(.*)'%args.trim , line)
-
- # add id and features
- if (mobj):
- record[nrec].id=mobj.group(1)
- record[nrec].features=mobj.group(2)
- inseq=0
- else :
- if inseq==0 :
- inseq=1
- record[nrec].seq = line
- else:
- cstring=record[nrec].seq+line
- record[nrec].seq = cstring
-sys.stdout.write("DONE\n")
-
-## ID FILTER LIST ##
-
-if (args.filter):
- sys.stdout.write("Filtering FASTA file...")
- id_filter=[line.rstrip('\n') for line in open(args.filter)]
- sys.stdout.write("DONE\n")
-
-
-## OUTPUT FASTA FILE ##
-
-if (args.output):
- sys.stdout.write("Writing FASTA file...")
- with open(args.output, 'w') as output:
- if (args.filter) and args.mode == 'k':
- if (args.remove):
- for x in range(0,nrec+1):
- if record[x].id in id_filter and (len(record[x].seq)-1 <= args.remove):
- output.write(">%s\n%s"%(record[x].id, record[x].seq))
- else:
- for x in range(0,nrec+1):
- if record[x].id in id_filter:
- output.write(">%s\n%s"%(record[x].id, record[x].seq))
- elif (args.filter) and args.mode == 'd':
- if (args.remove):
- for x in range(0,nrec+1):
- if record[x].id not in id_filter and (len(record[x].seq)-1 <= args.remove):
- output.write(">%s\n%s"%(record[x].id, record[x].seq))
- else:
- for x in range(0,nrec+1):
- if record[x].id not in id_filter:
- output.write(">%s\n%s"%(record[x].id, record[x].seq))
- else:
- if (args.remove):
- for x in range(0,nrec+1):
- if (len(record[x].seq)-1 <= args.remove):
- output.write(">%s\n%s"%(record[x].id, record[x].seq))
- else:
- for x in range(0,nrec+1):
- output.write(">%s\n%s"%(record[x].id, record[x].seq))
- output.close()
- sys.stdout.write("DONE\n")
-
-
-## OUTPUT LIST IDs ##
-
-idlist=[]
-if (args.idlist):
- sys.stdout.write("Creating IDs list from FASTA file...")
- fasta = open(args.output, 'r')
- with open(args.idlist, 'w') as id_list:
- for line in fasta:
- if line.startswith('>'):
- idlist.append(line[1:])
- idlist.sort()
- id_list.write(''.join(idlist))
- id_list.close()
- sys.stdout.write("DONE\n")
-
-
diff --git a/scripts/validation_gtf.py b/scripts/validation_gtf.py
deleted file mode 100755
index 515bcd7a427f30b268760620c2bc003d82b24f29..0000000000000000000000000000000000000000
--- a/scripts/validation_gtf.py
+++ /dev/null
@@ -1,180 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-import re
-import HTSeq
-from argparse import ArgumentParser
-
-### Created: Mar 5, 2019
-### Author: Paula Iborra
-### Company: Zavolan Group, Biozentrum, University of Basel
-
-
-### ARGUMENTS ###
-
-parser = ArgumentParser(
- description='Script to filter GTF files'
- )
-parser.add_argument(
- '-v','--version',
- action='version',
- version='%(prog)s 1.0',
- help='Show program\'s version number and exit'
- )
-parser.add_argument(
- '--idfield',
- help='Name of field that contains ID of interest. Default: transcript_id',
- default='transcript_id',
- choices=('transcript_id','gene_id', 'exon_id'),
- )
-parser.add_argument(
- '--idlist',
- help='Generate text file with one ID per line'
- )
-parser.add_argument(
- '-f','--filter',
- help='Remove IDs from GTF file missing in filter file. Filter file must contain ONE ID per line'
- )
-parser.add_argument(
- '-i','--input',
- required=True,
- help='Input GTF file',
- type=str
- )
-parser.add_argument(
- '-o','--output',
- required=True,
- help='Output GTF file'
- )
-
-args = parser.parse_args()
-
-#list filtered IDs
-ids = []
-
-### PARSE GTF FILE ###
-
-sys.stdout.write('Parsing GTF file...')
-
-# parse gtf file
-gtf_file = HTSeq.GFF_Reader(args.input)
-sys.stdout.write('DONE\n')
-
-### FILTER GTF ###
-# keep everyline not containing the id field, and the ones that contains the id field if id in id_filter list.
-
-if (args.filter):
- sys.stdout.write('Filtering GTF file - Step 1...')
-
- #open filter file and make it a list
- id_filter=[line.rstrip('\n') for line in open(args.filter)]
-
- pregtf = open('pregtf.gtf', 'w')
-
- for gtf_line in gtf_file:
- if gtf_line.type in ['gene', 'transcript', 'exon']:
- ## filter by gene_id
- if args.idfield == 'gene_id':
- if gtf_line.attr['gene_id'] in id_filter:
- pregtf.write(gtf_line.get_gff_line())
-
- ## filter by anything else
- else:
- if args.idfield not in gtf_line.attr.keys():
- pregtf.write(gtf_line.get_gff_line())
-
- else:
- if gtf_line.attr[args.idfield] in id_filter:
- pregtf.write(gtf_line.get_gff_line())
-
- pregtf.close()
- sys.stdout.write('DONE\n')
-
-### OUTPUT GTF FILE ###
-# remove those lines with no childs (empty genes / transcripts)
-
- sys.stdout.write('Filtering/Writing GTF file - Step 2...')
- pregtf = open('pregtf.gtf', 'r')
- gtf_output = open(args.output, 'w')
- previous = []
-
- if args.idfield == 'gene_id':
- for line in pregtf:
- gtf_output.write(line)
-
- elif args.idfield == 'transcript_id':
- # store first line
- if pregtf:
- first_line = pregtf.readline().split('\t')
- previous.append(first_line)
-
- for line in pregtf:
- line=line.split('\t')
-
- if line[2] == previous[-1][2]:
- if line[2] != 'gene':
- gtf_output.write('\t'.join(previous[-1]))
- del previous[-1]
- previous.append(line)
- else:
- del previous[-1]
- previous.append(line)
- else:
- gtf_output.write('\t'.join(previous[-1]))
- del previous[-1]
- previous.append(line)
-
- #for last line
- if previous[-1][2] == 'exon':
- gtf_output.write('\t'.join(previous[-1]))
-
- elif args.idfield == 'exon_id':
- for line in reversed(open('pregtf.gtf','r').readlines()):
- line = line.split('\t')
- if line[2] == 'exon':
- previous.append(line)
- else:
- if len(previous) == 0:
- continue
- else:
- if line[2] == 'transcript':
- if previous[-1][2] == 'exon':
- previous.append(line)
- elif line[2] == 'gene':
- if previous[-1][2] == 'transcript':
- previous.append(line)
- else:
- print('FILTER ERROR')
- break
- for i in previous[::-1]:
- gtf_output.write('\t'.join(i))
-
- gtf_output.close()
- sys.stdout.write('DONE\n')
-
-
-### OUTPUT IDs GTF FILE ###
-
-if (args.idlist):
- sys.stdout.write('Creating IDs list from GTF file...')
- ids_list = open(args.idlist, 'w')
- t = (re.match(r'([^_]*)',args.idfield)).group()
-
- # creating list of ids from gtf output filtered
- if (args.filter):
- gtf_output = HTSeq.GFF_Reader(args.output)
- for line in gtf_output:
- if line.type == t:
- ids_list.write(line.attr[args.idfield]+'\n')
- ids_list.close()
-
- # creating list of ids from input gtf file
- else:
- for line in gtf_file:
- if line.type == t:
- ids_list.write(line.attr[args.idfield]+'\n')
- ids_list.close()
-
- sys.stdout.write('DONE\n')
-
-
diff --git a/snakemake/Snakefile b/snakemake/Snakefile
index 43009bd56f0b59b35db87a18adf9cc56066d2362..069b8ade6f20eee8e76dd3487b27443724455f53 100644
--- a/snakemake/Snakefile
+++ b/snakemake/Snakefile
@@ -7,36 +7,36 @@ localrules: finish, genome_process, filter_anno_gtf
#################################################################################
rule finish:
- input:
- idx_transcriptome = expand(os.path.join(config["output_dir"], "{organism}", "{prefix_name}","transcriptome_index_segemehl.idx"),
- organism=config["organism"], prefix_name=config["prefix_name"]),
- idx_genome = expand(os.path.join(config["output_dir"],"{organism}", "{prefix_name}", "genome_index_segemehl.idx"),
- organism=config["organism"], prefix_name=config["prefix_name"]),
- exons = expand(os.path.join(config["output_dir"],"{organism}", "{prefix_name}", "exons.bed"),
- organism=config["organism"], prefix_name=config["prefix_name"]),
- header = expand(os.path.join(config["output_dir"],"{organism}", "{prefix_name}","headerOfCollapsedFasta.sam"),
- organism=config["organism"], prefix_name=config["prefix_name"]),
+ input:
+ idx_transcriptome = expand(os.path.join(config["output_dir"], "{organism}", "{prefix_name}","transcriptome_index_segemehl.idx"),
+ organism=config["organism"], prefix_name=config["prefix_name"]),
+ idx_genome = expand(os.path.join(config["output_dir"],"{organism}", "{prefix_name}", "genome_index_segemehl.idx"),
+ organism=config["organism"], prefix_name=config["prefix_name"]),
+ exons = expand(os.path.join(config["output_dir"],"{organism}", "{prefix_name}", "exons.bed"),
+ organism=config["organism"], prefix_name=config["prefix_name"]),
+ header = expand(os.path.join(config["output_dir"],"{organism}", "{prefix_name}","headerOfCollapsedFasta.sam"),
+ organism=config["organism"], prefix_name=config["prefix_name"]),
#################################################################################
### Download and process genome IDs
#################################################################################
rule genome_process:
- input:
- script = os.path.join(config["scripts_dir"],"genome_process.sh"),
- output:
- genome = os.path.join(config["output_dir"],"{organism}","{prefix_name}", "genome.processed.fa")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","genome_process.log"),
- prefix = config["prefix_name"],
- url = config["genome_url"],
- organism=config["organism"]
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}","genome_process.log")
- singularity:
- "docker://zavolab/ubuntu:18.04"
- shell:
- "(bash {input.script} {params.prefix} {params.organism} {params.url}) &> {log}"
+ input:
+ script = os.path.join(config["scripts_dir"],"genome_process.sh"),
+ output:
+ genome = os.path.join(config["output_dir"],"{organism}","{prefix_name}", "genome.processed.fa")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","genome_process.log"),
+ prefix = config["prefix_name"],
+ url = config["genome_url"],
+ organism=config["organism"]
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}","genome_process.log")
+ singularity:
+ "docker://zavolab/ubuntu:18.04"
+ shell:
+ "(bash {input.script} {params.prefix} {params.organism} {params.url}) &> {log}"
#################################################################################
@@ -44,40 +44,40 @@ rule genome_process:
#################################################################################
rule filter_anno_gtf:
- input:
- script = os.path.join(config["scripts_dir"],"filter_anno_gtf.sh"),
- output:
- gtf = os.path.join(config["output_dir"],"{organism}","{prefix_name}","gene_annotations.filtered.gtf")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","download_filter_gtf.log"),
- prefix = config["prefix_name"],
- url = config["gtf_url"],
- organism=config["organism"]
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}","filter_anno_gtf.log")
- singularity:
- "docker://zavolab/ubuntu:18.04"
- shell:
- "(bash {input.script} {params.prefix} {params.organism} {params.url}) &> {log}"
+ input:
+ script = os.path.join(config["scripts_dir"],"filter_anno_gtf.sh"),
+ output:
+ gtf = os.path.join(config["output_dir"],"{organism}","{prefix_name}","gene_annotations.filtered.gtf")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","download_filter_gtf.log"),
+ prefix = config["prefix_name"],
+ url = config["gtf_url"],
+ organism=config["organism"]
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}","filter_anno_gtf.log")
+ singularity:
+ "docker://zavolab/ubuntu:18.04"
+ shell:
+ "(bash {input.script} {params.prefix} {params.organism} {params.url}) &> {log}"
#################################################################################
### Extract transcriptome sequences in FASTA from genome.
#################################################################################
rule extract_transcriptome_seqs:
- input:
- genome = os.path.join(config["output_dir"],"{organism}","{prefix_name}", "genome.processed.fa"),
- gtf = os.path.join(config["output_dir"],"{organism}","{prefix_name}","gene_annotations.filtered.gtf")
- output:
- fasta = os.path.join(config["output_dir"],"{organism}","{prefix_name}","transcriptome.fa")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","extract_transcriptome_seqs.log")
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}","extract_transcriptome_seqs.log")
- singularity:
- "docker://zavolab/cufflinks:2.2.1"
- shell:
- "(gffread -w {output.fasta} -g {input.genome} {input.gtf}) &> {log}"
+ input:
+ genome = os.path.join(config["output_dir"],"{organism}","{prefix_name}", "genome.processed.fa"),
+ gtf = os.path.join(config["output_dir"],"{organism}","{prefix_name}","gene_annotations.filtered.gtf")
+ output:
+ fasta = os.path.join(config["output_dir"],"{organism}","{prefix_name}","transcriptome.fa")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","extract_transcriptome_seqs.log")
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}","extract_transcriptome_seqs.log")
+ singularity:
+ "docker://zavolab/cufflinks:2.2.1"
+ shell:
+ "(gffread -w {output.fasta} -g {input.genome} {input.gtf}) &> {log}"
################################################################################
@@ -85,17 +85,18 @@ rule extract_transcriptome_seqs:
################################################################################
rule trim_fasta:
- input:
- fasta = os.path.join(config["output_dir"], "{organism}","{prefix_name}","transcriptome.fa"),
- script = os.path.join(config["scripts_dir"], "validation_fasta.py")
- output:
- fasta = os.path.join(config["output_dir"],"{organism}","{prefix_name}","transcriptome_idtrim.fa")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","trim_fasta.log")
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}","trim_fasta.log")
- shell:
- "(python {input.script} --trim -i {input.fasta} -o {output.fasta}) &> {log}"
+ input:
+ fasta = os.path.join(config["output_dir"], "{organism}","{prefix_name}","transcriptome.fa"),
+ output:
+ fasta = os.path.join(config["output_dir"],"{organism}","{prefix_name}","transcriptome_idtrim.fa")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","trim_fasta.log")
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}","trim_fasta.log")
+ singularity:
+ "docker://zavolab/ubuntu:18.04"
+ shell:
+ """(awk -F" " "/^>/ {{print \$1; next}} 1" {input.fasta} > {output.fasta}) &> {log}"""
#################################################################################
@@ -103,22 +104,22 @@ rule trim_fasta:
#################################################################################
rule generate_segemehl_index_transcriptome:
- input:
- fasta = os.path.join(config["output_dir"],"{organism}","{prefix_name}","transcriptome_idtrim.fa")
- output:
- idx = os.path.join(config["output_dir"],"{organism}","{prefix_name}","transcriptome_index_segemehl.idx")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","generate_segemehl_index_transcriptome.log"),
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}","generate_segemehl_index_transcriptome.log")
- resources:
- mem = 10,
- threads = 8,
- time = 6
- singularity:
- "docker://zavolab/segemehl:0.2.0"
- shell:
- "(segemehl.x -x {output.idx} -d {input.fasta}) &> {log}"
+ input:
+ fasta = os.path.join(config["output_dir"],"{organism}","{prefix_name}","transcriptome_idtrim.fa")
+ output:
+ idx = os.path.join(config["output_dir"],"{organism}","{prefix_name}","transcriptome_index_segemehl.idx")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","generate_segemehl_index_transcriptome.log"),
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}","generate_segemehl_index_transcriptome.log")
+ resources:
+ mem = 10,
+ threads = 8,
+ time = 6
+ singularity:
+ "docker://zavolab/segemehl:0.2.0"
+ shell:
+ "(segemehl.x -x {output.idx} -d {input.fasta}) &> {log}"
#################################################################################
@@ -126,24 +127,24 @@ rule generate_segemehl_index_transcriptome:
#################################################################################
rule generate_segemehl_index_genome:
- input:
- #genome = config["genome"]
- genome = os.path.join(config["output_dir"],"{organism}","{prefix_name}", "genome.processed.fa")
-
- output:
- idx = os.path.join(config["output_dir"],"{organism}","{prefix_name}","genome_index_segemehl.idx")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","generate_segemehl_index_genome.log"),
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}","generate_segemehl_index_genome.log")
- resources:
- mem = 60,
- threads = 8,
- time = 6
- singularity:
- "docker://zavolab/segemehl:0.2.0"
- shell:
- "(segemehl.x -x {output.idx} -d {input.genome}) &> {log}"
+ input:
+ #genome = config["genome"]
+ genome = os.path.join(config["output_dir"],"{organism}","{prefix_name}", "genome.processed.fa")
+
+ output:
+ idx = os.path.join(config["output_dir"],"{organism}","{prefix_name}","genome_index_segemehl.idx")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","generate_segemehl_index_genome.log"),
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}","generate_segemehl_index_genome.log")
+ resources:
+ mem = 60,
+ threads = 8,
+ time = 6
+ singularity:
+ "docker://zavolab/segemehl:0.2.0"
+ shell:
+ "(segemehl.x -x {output.idx} -d {input.genome}) &> {log}"
#################################################################################
@@ -151,19 +152,19 @@ rule generate_segemehl_index_genome:
#################################################################################
rule get_exons_gtf:
- input:
- gtf = os.path.join(config["output_dir"],"{organism}","{prefix_name}","gene_annotations.filtered.gtf"),
- script = os.path.join(config["scripts_dir"], "get_lines_w_pattern.sh")
- output:
- exons = os.path.join(config["output_dir"],"{organism}","{prefix_name}","exons.gtf")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","get_exons_gtf.log")
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}", "get_exons_gtf.log")
- singularity:
- "docker://zavolab/ubuntu:18.04"
- shell:
- "(bash {input.script} -f {input.gtf} -c 3 -p exon -o {output.exons} ) &> {log}"
+ input:
+ gtf = os.path.join(config["output_dir"],"{organism}","{prefix_name}","gene_annotations.filtered.gtf"),
+ script = os.path.join(config["scripts_dir"], "get_lines_w_pattern.sh")
+ output:
+ exons = os.path.join(config["output_dir"],"{organism}","{prefix_name}","exons.gtf")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","get_exons_gtf.log")
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}", "get_exons_gtf.log")
+ singularity:
+ "docker://zavolab/ubuntu:18.04"
+ shell:
+ "(bash {input.script} -f {input.gtf} -c 3 -p exon -o {output.exons} ) &> {log}"
#################################################################################
@@ -171,19 +172,19 @@ rule get_exons_gtf:
#################################################################################
rule gtftobed:
- input:
- exons = os.path.join(config["output_dir"],"{organism}","{prefix_name}","exons.gtf"),
- script = os.path.join(config["scripts_dir"], "gtf_exons_bed.1.1.2.R")
- output:
- exons = os.path.join(config["output_dir"],"{organism}","{prefix_name}","exons.bed")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","gtftobed.log")
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}","gtftobed.log")
- singularity:
- "docker://zavolab/r-zavolab:3.5.1"
- shell:
- "(Rscript {input.script} --gtf {input.exons} -o {output.exons}) &> {log}"
+ input:
+ exons = os.path.join(config["output_dir"],"{organism}","{prefix_name}","exons.gtf"),
+ script = os.path.join(config["scripts_dir"], "gtf_exons_bed.1.1.2.R")
+ output:
+ exons = os.path.join(config["output_dir"],"{organism}","{prefix_name}","exons.bed")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","gtftobed.log")
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}","gtftobed.log")
+ singularity:
+ "docker://zavolab/r-zavolab:3.5.1"
+ shell:
+ "(Rscript {input.script} --gtf {input.exons} -o {output.exons}) &> {log}"
#################################################################################
@@ -191,16 +192,16 @@ rule gtftobed:
#################################################################################
rule create_header_genome:
- input:
- #genome = config["genome"]
- genome = os.path.join(config["output_dir"],"{organism}","{prefix_name}", "genome.processed.fa")
- output:
- header = os.path.join(config["output_dir"],"{organism}","{prefix_name}","headerOfCollapsedFasta.sam")
- params:
- cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","create_header_genome.log")
- log:
- os.path.join(config["local_log"],"{organism}","{prefix_name}","create_header_genome.log")
- singularity:
- "docker://zavolab/samtools:1.8"
- shell:
- "(samtools dict -o {output.header} {input.genome}) &> {log}"
+ input:
+ #genome = config["genome"]
+ genome = os.path.join(config["output_dir"],"{organism}","{prefix_name}", "genome.processed.fa")
+ output:
+ header = os.path.join(config["output_dir"],"{organism}","{prefix_name}","headerOfCollapsedFasta.sam")
+ params:
+ cluster_log = os.path.join(config["cluster_log"],"{organism}","{prefix_name}","create_header_genome.log")
+ log:
+ os.path.join(config["local_log"],"{organism}","{prefix_name}","create_header_genome.log")
+ singularity:
+ "docker://zavolab/samtools:1.8"
+ shell:
+ "(samtools dict -o {output.header} {input.genome}) &> {log}"
diff --git a/snakemake/snakemake_unused_rules b/snakemake/snakemake_unused_rules
deleted file mode 100644
index f34d654900148210095340a25c5f64d88123bae1..0000000000000000000000000000000000000000
--- a/snakemake/snakemake_unused_rules
+++ /dev/null
@@ -1,56 +0,0 @@
-#################################################################################
-### DOWNLOAD DATA
-#################################################################################
-
-# rule download_files:
-# input:
-# files = config["input_files"]
-# output:
-# files = config["download_directory"]
-# params:
-# type = config["download_type"]
-# log:
-# os.path.join(config["local_log"], "download_files.log")
-# shell:
-# "(python scripts/download_files.py {}) &> {log}"
-
-
-#################################################################################
-### Filter GTF and get ID list
-#################################################################################
-
-# rule filter_gtf:
-# input:
-# idlist = os.path.join(config["output_dir"], "idlist_fasta.txt"),
-# gtf = config["gtf"],
-# script = os.path.join(config["scripts_dir"], "validation_gtf.py")
-# output:
-# idlist = os.path.join(config["output_dir"], "idlist_gtf.txt"),
-# gtf = os.path.join(config["output_dir"], "gtf_filtered.gtf")
-# params:
-# cluster_log = os.path.join(config["cluster_log"], "filter_gtf.log")
-# singularity:
-# "docker://zavolab/python_htseq:3.6.5_0.10.0"
-# log:
-# os.path.join(config["local_log"], "filter_gtf.log")
-# shell:
-# "(python {input.script} --idlist {output.idlist} -f {input.idlist} -i {input.gtf} -o {output.gtf}) &> {log}"
-
-
-#################################################################################
-### Filter FASTA file
-#################################################################################
-
-# rule filter_fasta:
-# input:
-# fasta = os.path.join(config["output_dir"], "transcriptome_idtrim.fa"),
-# idlist = os.path.join(config["output_dir"], "idlist_gtf.txt"),
-# script = os.path.join(config["scripts_dir"], "validation_fasta.py")
-# output:
-# fasta = os.path.join(config["output_dir"], "transcriptome_filtered.fa")
-# params:
-# cluster_log = os.path.join(config["cluster_log"], "filter_fasta.log")
-# log:
-# os.path.join(config["local_log"], "filter_fasta.log")
-# shell:
-# "(python {input.script} --filter {input.idlist} -i {input.fasta} -o {output.fasta}) &> {log}"