annotate extract_features.py @ 10:0fc0f9cf035a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 69d542836dbce9261906bb0d1e7ef39f9712f4a3

#!/usr/bin/env python

import argparse
import sys
import textwrap


def main(args):
    """
        Extract the protein and coding section from an augustus gff, gtf file
        Example file:
    HS04636	AUGUSTUS	stop_codon	6901	6903	.	+	0	Parent=g1.t1
    HS04636	AUGUSTUS	transcription_end_site	8857	8857	.	+	.	Parent=g1.t1
    # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
    # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
    # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
    # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
    # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
    # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
    # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
    # end gene g1
    ###
    #
    # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
    #
    # Predicted genes for sequence number 2 on both strands
    # start gene g2
    HS08198	AUGUSTUS	gene	86	2344	1	+	.	ID=g2
    HS08198	AUGUSTUS	transcript	86	2344	.	+	.	ID=g2.t1;Parent=g2
    HS08198	AUGUSTUS	transcription_start_site	86	86	.	+	.	Parent=g2.t1
    HS08198	AUGUSTUS	exon	86	582	.	+	.	Parent=g2.t1
    HS08198	AUGUSTUS	start_codon	445	447	.	+	0	Parent=g2.t1
    """
    protein_seq = ""
    coding_seq = ""
    if args.protein:
        po = open(args.protein, "w+")
    if args.codingseq:
        co = open(args.codingseq, "w+")

    for line in sys.stdin:
        # protein- and coding-sequence are stored as comments
        if line.startswith("#"):
            line = line[2:].strip()
            if line.startswith("start gene"):
                gene_name = line[11:].strip()

            if protein_seq:
                if line.endswith("]"):
                    protein_seq += line[:-1]
                    po.write(
                        ">%s\n%s\n"
                        % (gene_name, "\n".join(textwrap.wrap(protein_seq, 80)))
                    )
                    protein_seq = ""
                else:
                    protein_seq += line

            if coding_seq:
                if line.endswith("]"):
                    coding_seq += line[:-1]
                    co.write(
                        ">%s\n%s\n"
                        % (gene_name, "\n".join(textwrap.wrap(coding_seq, 80)))
                    )
                    coding_seq = ""
                else:
                    coding_seq += line

            if args.protein and line.startswith("protein sequence = ["):
                if line.endswith("]"):
                    protein_seq = line[20:-1]
                    po.write(
                        ">%s\n%s\n"
                        % (gene_name, "\n".join(textwrap.wrap(protein_seq, 80)))
                    )
                    protein_seq = ""
                else:
                    line = line[20:]
                    protein_seq = line

            if args.codingseq and line.startswith("coding sequence = ["):
                if line.endswith("]"):
                    coding_seq = line[19:-1]
                    co.write(
                        ">%s\n%s\n"
                        % (gene_name, "\n".join(textwrap.wrap(coding_seq, 80)))
                    )
                    coding_seq = ""
                else:
                    line = line[19:]
                    coding_seq = line

    if args.codingseq:
        co.close()
    if args.protein:
        po.close()


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument("-p", "--protein", help="Path to the protein file.")
    parser.add_argument("-c", "--codingseq", help="Path to the coding file.")

    args = parser.parse_args()
    main(args)