Merge branch '15-split-fasta-chunks' into 'master'

Split a FASTA file in chunks

Closes #15

See merge request !2

tools/utils/split_fasta/Snakefile

+rule split_fasta:
+    """
+    Split a FASTA file with the desired number of sequences per chunk
+    """
+    input:
+        __split_fasta_input
+    output:
+        __split_fasta_output
+    params:
+        n_lines = __split_fasta_number_sequences * 2,
+        prefix = __split_fasta_prefix
+    shell:
+        """
+        cat {input} | awk '/^>/ {{if(N>0) printf("\\n"); printf("%s\\n",$0);++N;next;}} {{ printf("%s",$0);}} END {{printf("\\n");}}' | split -l {params.n_lines} -a 5 -d - {params.prefix}
+        for i in `ls {params.prefix}*`; do mv $i ${{i}}.fa;done
+        """

tools/utils/split_fasta/example_usage/Snakefile

+configfile: "config.yaml"
+
+def count_sequences(fasta_file):
+    with open(fasta_file, 'r') as file:
+        seq = 0
+        for line in file:
+            if '>' in line:
+                seq += 1
+    return seq
+
+# ==== Snakefile path ====
+__split_fasta_rules = config.get("snakefiles", {}).get("split_fasta")
+
+__main_output_dir = config.get('output_dir', 'output')
+
+# ==== Split FASTA ====
+__split_fasta_output_dir = __main_output_dir +  "/split_fasta"
+
+__split_fasta_input = config['input_fasta']
+__split_fasta_number_sequences = config.get('split_fasta', {}).get('number_sequences', 1000000)
+total_number_sequences = count_sequences(__split_fasta_input)
+EXTENSIONS = [f"{i:05d}" for i in range(0, int(total_number_sequences/__split_fasta_number_sequences) + 1)]
+__split_fasta_prefix = "/".join([__split_fasta_output_dir, config['split_fasta']['prefix']])
+__split_fasta_output = expand(__split_fasta_prefix + "{ext}.fa", ext=EXTENSIONS)
+include: __split_fasta_rules
+
+rule all:
+    input: __split_fasta_output

tools/utils/split_fasta/example_usage/config.yaml

+snakefiles:
+    split_fasta: /pasteur/projets/policy01/Atm/snakemake/tools/utils/split_fasta/Snakefile
+
+input_fasta: /pasteur/projets/policy01/DBs/IGC/2014-9.9M/IGC.fa
+output_dir: /pasteur/projets/policy01/sandbox/20200210_test_snakemake/output
+
+split_fasta:
+    prefix: IGC_
+    number_sequences: 1000000