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Merge pull request #26 from nigyta/genemarkS2
Added options to enable GeneMarkS2, Diamond, RNAmmer
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| Original file line number | Diff line number | Diff line change |
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@@ -7,3 +7,4 @@ __pycache__/ | |
| db/* | ||
| !bin/Darwin/barrnap-0.8/db/ | ||
| !db/hmm_search/ | ||
| OUT/ | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1 +1 @@ | ||
| dfast_version = "1.2.5" | ||
| dfast_version = "1.2.6" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,112 @@ | ||
| #! /usr/bin/env python | ||
| # coding: UTF8 | ||
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| # Written by Aaron Pfennig | ||
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| from .base_tools import StructuralAnnotationTool | ||
| from Bio import SeqIO | ||
| from ..models.bio_feature import ExtendedFeature | ||
| import os.path | ||
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| class GeneMarkS2(StructuralAnnotationTool): | ||
| """ | ||
| GeneMarkS2 | ||
| Tool type: CDS prediction | ||
| URL: | ||
| REF: | ||
| """ | ||
| version = None | ||
| TYPE = "CDS" | ||
| NAME = "GeneMarkS2" | ||
| VERSION_CHECK_CMD = ["gms2.pl | tail -n 1"] | ||
| VERSION_PATTERN = r"Version: (.+)_lic" | ||
| SHELL = True | ||
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| def __init__(self, options=None, workDir="OUT"): | ||
| super(GeneMarkS2, self).__init__(options, workDir) | ||
| self.transl_table = options.get("transl_table", 11) | ||
| self.out_format = options.get("format", "gff") | ||
| self.genome_type = options.get("genome_type", "bacteria") | ||
| self.cmd_options = options.get("cmd_options", "") | ||
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| def getCommand(self): | ||
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| # /home/apfennig3/Team1-GenePrediction/bin/gms2.pl --seq $genome --genome-type bacteria --output $tmp_dir/output.gtf --format gff | ||
| # GeneMarkS2 generates a log file in the current directory. | ||
| # To avoid leaving a log file, GeneMarkS2 is run aftr changing the directory. | ||
| gms2_work_dir = os.path.dirname(self.outputFile) | ||
| rel_input_file = os.path.join("..", "input", os.path.basename(self.genomeFasta)) | ||
| output_file = os.path.basename(self.outputFile) | ||
| cmd = ["cd", gms2_work_dir, ";", "gms2.pl", self.cmd_options, "--genome-type", | ||
| self.genome_type, "--gcode", str(self.transl_table), "--format", self.out_format, "--seq", rel_input_file, "--output", output_file] | ||
| # cmd = ["gms2.pl", self.cmd_options, "--genome-type", self.genome_type, "--gcode", str(self.transl_table), "--format", self.out_format, "--seq", self.genomeFasta, "--output", self.outputFile] | ||
| return cmd | ||
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| def getFeatures(self): | ||
| """GeneMarkS2 generates standard GFF format. | ||
| """ | ||
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| def _parseResult(): | ||
| with open(self.outputFile) as f: | ||
| for line in f: | ||
| if line.startswith("#"): | ||
| continue | ||
| # Genemark has an empty line between header and actual predictions | ||
| if len(line) == 1: | ||
| continue | ||
| sequence, toolName, featureType, left, right, score, strand, _, qualifiers = line.strip("\n").split("\t") | ||
| qualifiers = dict([x.split(' ') for x in qualifiers.strip(";").split("; ")]) | ||
| yield sequence, toolName, featureType, left, right, strand, qualifiers | ||
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| def _getLengthDict(fileName): | ||
| R = list(SeqIO.parse(open(fileName), "fasta")) | ||
| return {r.id: len(r) for r in R} | ||
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| def _get_feature(left, right, strand, partial_flag, seq_length, i): | ||
| left_flag, right_flag = partial_flag[0], partial_flag[1] | ||
| left, right, codon_start = int(left), int(right), 1 | ||
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| if left_flag == "1" and left <= 3: | ||
| if strand == "+": | ||
| codon_start = left | ||
| left = 1 | ||
| if right_flag == "1" and seq_length - right <= 2: | ||
| if strand == "-": | ||
| codon_start = seq_length - right + 1 | ||
| right = seq_length | ||
| location = self.getLocation(left, right, strand, partial_flag) | ||
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| annotations = {"partial_flag": partial_flag} | ||
| if partial_flag != "00": | ||
| annotations["partial"] = True | ||
| feature = ExtendedFeature(location=location, type="CDS", id="{0}_{1}".format(self.__class__.__name__, i), | ||
| seq_id=sequence, annotations=annotations) | ||
| feature.qualifiers = { | ||
| "product": ["hypothetical protein"], | ||
| "inference": ["COORDINATES:ab initio prediction:{0}:{1}".format(self.NAME, self.version)], | ||
| "transl_table": [str(self.transl_table)], | ||
| "codon_start": [codon_start] | ||
| } | ||
| return feature | ||
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| dict_length = _getLengthDict(self.genomeFasta) | ||
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| D = {} | ||
| i = 0 | ||
| for sequence, toolName, featureType, left, right, strand, qualifiers in _parseResult(): | ||
| partial_flag = qualifiers.get("partial", "00") | ||
| seq_length = dict_length[sequence] | ||
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| i += 1 | ||
| feature = _get_feature(left, right, strand, partial_flag, seq_length, i) | ||
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| if qualifiers.get("rbs_motif", "None") != "None": | ||
| feature.annotations["rbs"] = qualifiers["rbs_motif"] | ||
| D.setdefault(sequence, []).append(feature) | ||
| return D | ||
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