augustus: extract_features.py annotate

annotate extract_features.py @ 4:4de31938431b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e

author	iuc
date	Fri, 20 Oct 2017 03:48:57 -0400
parents	af307d3285c5
children	09855551d713

rev	line source
0 af307d3285c5 Uploaded bgruening parents: diff changeset	1 #!/usr/bin/env python
af307d3285c5 Uploaded bgruening parents: diff changeset	2
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	3 import argparse
0 af307d3285c5 Uploaded bgruening parents: diff changeset	4 import sys
af307d3285c5 Uploaded bgruening parents: diff changeset	5 import textwrap
af307d3285c5 Uploaded bgruening parents: diff changeset	6
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	7
0 af307d3285c5 Uploaded bgruening parents: diff changeset	8 def main( args ):
af307d3285c5 Uploaded bgruening parents: diff changeset	9 """
af307d3285c5 Uploaded bgruening parents: diff changeset	10 Extract the protein and coding section from an augustus gff, gtf file
af307d3285c5 Uploaded bgruening parents: diff changeset	11 Example file:
af307d3285c5 Uploaded bgruening parents: diff changeset	12 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
af307d3285c5 Uploaded bgruening parents: diff changeset	13 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1
af307d3285c5 Uploaded bgruening parents: diff changeset	14 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
af307d3285c5 Uploaded bgruening parents: diff changeset	15 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
af307d3285c5 Uploaded bgruening parents: diff changeset	16 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
af307d3285c5 Uploaded bgruening parents: diff changeset	17 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
af307d3285c5 Uploaded bgruening parents: diff changeset	18 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
af307d3285c5 Uploaded bgruening parents: diff changeset	19 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
af307d3285c5 Uploaded bgruening parents: diff changeset	20 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
af307d3285c5 Uploaded bgruening parents: diff changeset	21 # end gene g1
af307d3285c5 Uploaded bgruening parents: diff changeset	22 ###
af307d3285c5 Uploaded bgruening parents: diff changeset	23 #
af307d3285c5 Uploaded bgruening parents: diff changeset	24 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
af307d3285c5 Uploaded bgruening parents: diff changeset	25 #
af307d3285c5 Uploaded bgruening parents: diff changeset	26 # Predicted genes for sequence number 2 on both strands
af307d3285c5 Uploaded bgruening parents: diff changeset	27 # start gene g2
af307d3285c5 Uploaded bgruening parents: diff changeset	28 HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2
af307d3285c5 Uploaded bgruening parents: diff changeset	29 HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2
af307d3285c5 Uploaded bgruening parents: diff changeset	30 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1
af307d3285c5 Uploaded bgruening parents: diff changeset	31 HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1
af307d3285c5 Uploaded bgruening parents: diff changeset	32 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1
af307d3285c5 Uploaded bgruening parents: diff changeset	33 """
af307d3285c5 Uploaded bgruening parents: diff changeset	34 protein_seq = ''
af307d3285c5 Uploaded bgruening parents: diff changeset	35 coding_seq = ''
af307d3285c5 Uploaded bgruening parents: diff changeset	36 if args.protein:
af307d3285c5 Uploaded bgruening parents: diff changeset	37 po = open( args.protein, 'w+' )
af307d3285c5 Uploaded bgruening parents: diff changeset	38 if args.codingseq:
af307d3285c5 Uploaded bgruening parents: diff changeset	39 co = open( args.codingseq, 'w+' )
af307d3285c5 Uploaded bgruening parents: diff changeset	40
af307d3285c5 Uploaded bgruening parents: diff changeset	41 for line in sys.stdin:
af307d3285c5 Uploaded bgruening parents: diff changeset	42 # protein- and coding-sequence are stored as comments
af307d3285c5 Uploaded bgruening parents: diff changeset	43 if line.startswith('#'):
af307d3285c5 Uploaded bgruening parents: diff changeset	44 line = line[2:].strip()
af307d3285c5 Uploaded bgruening parents: diff changeset	45 if line.startswith('start gene'):
af307d3285c5 Uploaded bgruening parents: diff changeset	46 gene_name = line[11:].strip()
af307d3285c5 Uploaded bgruening parents: diff changeset	47
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	48 if protein_seq:
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	49 if line.endswith(']'):
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	50 protein_seq += line[:-1]
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	51 po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	52 protein_seq = ''
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	53 else:
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	54 protein_seq += line
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	55
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	56 if coding_seq:
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	57 if line.endswith(']'):
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	58 coding_seq += line[:-1]
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	59 co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	60 coding_seq = ''
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	61 else:
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	62 coding_seq += line
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	63
0 af307d3285c5 Uploaded bgruening parents: diff changeset	64 if args.protein and line.startswith('protein sequence = ['):
af307d3285c5 Uploaded bgruening parents: diff changeset	65 if line.endswith(']'):
af307d3285c5 Uploaded bgruening parents: diff changeset	66 protein_seq = line[20:-1]
af307d3285c5 Uploaded bgruening parents: diff changeset	67 po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
af307d3285c5 Uploaded bgruening parents: diff changeset	68 protein_seq = ''
af307d3285c5 Uploaded bgruening parents: diff changeset	69 else:
af307d3285c5 Uploaded bgruening parents: diff changeset	70 line = line[20:]
af307d3285c5 Uploaded bgruening parents: diff changeset	71 protein_seq = line
af307d3285c5 Uploaded bgruening parents: diff changeset	72
af307d3285c5 Uploaded bgruening parents: diff changeset	73 if args.codingseq and line.startswith('coding sequence = ['):
af307d3285c5 Uploaded bgruening parents: diff changeset	74 if line.endswith(']'):
af307d3285c5 Uploaded bgruening parents: diff changeset	75 coding_seq = line[19:-1]
af307d3285c5 Uploaded bgruening parents: diff changeset	76 co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
af307d3285c5 Uploaded bgruening parents: diff changeset	77 coding_seq = ''
af307d3285c5 Uploaded bgruening parents: diff changeset	78 else:
af307d3285c5 Uploaded bgruening parents: diff changeset	79 line = line[19:]
af307d3285c5 Uploaded bgruening parents: diff changeset	80 coding_seq = line
af307d3285c5 Uploaded bgruening parents: diff changeset	81
af307d3285c5 Uploaded bgruening parents: diff changeset	82 if args.codingseq:
af307d3285c5 Uploaded bgruening parents: diff changeset	83 co.close()
af307d3285c5 Uploaded bgruening parents: diff changeset	84 if args.protein:
af307d3285c5 Uploaded bgruening parents: diff changeset	85 po.close()
af307d3285c5 Uploaded bgruening parents: diff changeset	86
4 4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: 0 diff changeset	87
0 af307d3285c5 Uploaded bgruening parents: diff changeset	88 if __name__ == '__main__':
af307d3285c5 Uploaded bgruening parents: diff changeset	89 parser = argparse.ArgumentParser()
af307d3285c5 Uploaded bgruening parents: diff changeset	90 parser.add_argument('-p', '--protein', help='Path to the protein file.')
af307d3285c5 Uploaded bgruening parents: diff changeset	91 parser.add_argument('-c', '--codingseq', help='Path to the coding file.')
af307d3285c5 Uploaded bgruening parents: diff changeset	92
af307d3285c5 Uploaded bgruening parents: diff changeset	93 args = parser.parse_args()
af307d3285c5 Uploaded bgruening parents: diff changeset	94 main( args )

Mercurial > repos > bgruening > augustus

annotate extract_features.py @ 4:4de31938431b draft