ngsplot: bin/ngsplotdb.py annotate

annotate bin/ngsplotdb.py @ 2:4b4d858c0aa9 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'3611708386b2a2495ac9daee71a32cd990f2aa16\n'-dirty

author	artbio
date	Fri, 08 Dec 2017 09:36:11 -0500
parents	3ca58369469c
children

rev	line source
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	1 #!/usr/bin/env python
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	2 #
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	3 # ngsplotdb - PYTHON script to manipulate the ngs.plot database installation.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	4 # Author: Li Shen, Mount Sinai School of Medicine
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	5 # Date created: Dec 28, 2012
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	6 # Last updated: May 28, 2013
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	7 #
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	8 # Functions implemented:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	9 #
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	10 # list - List locally installed genomes.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	11 # check - Check the integrity of local database.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	12 # install - Install a genome from ngsplotdb.XXX.tar.gz.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	13 # remove - Remove a locally installed genome.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	14
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	15
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	16 # def dir_to_idspec(dirn):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	17 # """Convert an FTP directory name to species ID and Name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	18 # This works with both UCSC and Ensembl FTP.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	19 # """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	20 # parts = dirn.split('_')
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	21 # sid = parts[0][:3].lower() + parts[1][:3].lower()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	22 # spec = str.title(parts[0] + ' ' + parts[1])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	23 # return sid, spec
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	24
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	25 # def listremote(database="refseq"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	26 # """List available genomes on a remote FTP site."""
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	27
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	28 # import urllib2
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	29
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	30 # url_ensembl = "ftp://ftp.ensembl.org/pub/current_gtf/"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	31 # url_ucsc = "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	32
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	33 # if database == "refseq":
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	34 # ftp = urllib2.urlopen(url_ucsc)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	35 # elif database == "ensembl":
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	36 # ftp = urllib2.urlopen(url_ensembl)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	37 # else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	38 # pass
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	39
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	40 # # Read directory names from the remote FTP site.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	41 # dir_names = ftp.read().splitlines()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	42 # # Parse lines to obtain clean directory names only.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	43 # if database == "refseq":
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	44 # dir_names = map(lambda x: x.split()[-3], dir_names)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	45 # elif database == "ensembl":
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	46 # dir_names = map(lambda x: x.split()[-1], dir_names)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	47 # else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	48 # pass
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	49 # # Filter directory names that do not correspond to a species.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	50 # # On UCSC FTP, both "." and ".." will be retrieved from above and can
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	51 # # cause troubles.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	52
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	53 # id_spec_list = map(dir_to_idspec, dir_names)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	54 # print "ID\tName"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	55 # for r in id_spec_list:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	56 # print r[0], "\t", r[1]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	57
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	58 def read_gnlist(root_path, mode):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	59 """Read installed genomes list.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	60
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	61 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	62 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	63 mode: row reading mode - "vector" or "hash", correspond to each record
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	64 read as a vector of hash table.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	65 Returns: (header split vector, hash table of installed genomes,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	66 vector of column widths)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	67 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	68 from collections import defaultdict
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	69
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	70 gn_list = root_path + "/database/gn_list.txt"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	71 try:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	72 db_f = open(gn_list, "r")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	73 except IOError:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	74 print "Open {0} error: your ngs.plot database may be corrupted.".\
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	75 format(gn_list)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	76 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	77
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	78 default_list = root_path + "/database/default.tbl"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	79 try:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	80 default_f = open(default_list, "r")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	81 except IOError:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	82 print "Open {0} error: your ngs.plot database may be corrupted.".\
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	83 format(default_list)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	84 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	85 default_l = []
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	86 header = default_f.readline() # skip the header
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	87 for rec in default_f:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	88 r_sp = rec.rstrip().split("\t")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	89 default_l.append((r_sp[0], r_sp[2])) # tuple of genome and region, like ("dm3", "genebody")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	90 genome_region_dict = defaultdict(list)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	91 for genome,region in default_l:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	92 genome_region_dict[genome].append(region)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	93
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	94 header = db_f.readline()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	95 h_sp = header.rstrip().split("\t")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	96 h_sp.append("InstalledFeatures")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	97 v_cw = map(len, h_sp) # column widths initialize to header widths.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	98
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	99 g_tbl = {}
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	100 for rec in db_f:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	101 r_sp = rec.rstrip().split("\t")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	102 r_sp.append(",".join(genome_region_dict[r_sp[0]]))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	103 r_cw = map(len, r_sp)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	104 v_cw = map(max, v_cw, r_cw)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	105
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	106 r_tbl = dict(zip(h_sp, r_sp))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	107 if(mode == "vector"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	108 g_tbl[r_tbl["ID"]] = r_sp
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	109 elif(mode == "hash"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	110 g_tbl[r_tbl["ID"]] = r_tbl
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	111 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	112 pass
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	113
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	114 db_f.close()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	115
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	116 return (h_sp, g_tbl, v_cw)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	117
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	118
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	119 def update_gnlist(root_path, g_tbl, gn, assembly, species, ens_v, np_v):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	120 """Update/Add genomes in ngs.plot database.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	121
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	122 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	123 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	124 g_tbl: genome hash table. Each value is also a hash table of
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	125 genome info.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	126 gn: genome name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	127 assembly: genome assembly name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	128 species: species name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	129 ens_v: new Ensembl version.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	130 np_v: new ngs.plot version.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	131 Returns: None
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	132 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	133
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	134 if gn in g_tbl:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	135 g_tbl[gn]["EnsVer"] = ens_v
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	136 g_tbl[gn]["NPVer"] = np_v
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	137 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	138 g_tbl[gn] = {"ID": gn, "Assembly": assembly, "Species": species, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	139 "EnsVer": ens_v, "NPVer": np_v}
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	140
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	141 write_gnlist(root_path, g_tbl)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	142
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	143
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	144 def write_gnlist(root_path, g_tbl):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	145 """Write genome hash table to database file: gn_list.txt.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	146
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	147 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	148 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	149 g_tbl: genome hash table. Each value is also a hash table of
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	150 genome info.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	151 Returns: None
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	152 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	153
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	154 output_order = ["ID", "Assembly", "Species", "EnsVer", "NPVer"]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	155 gn_list = root_path + "/database/gn_list.txt"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	156
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	157 try:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	158 db_f = open(gn_list, "w")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	159 except IOError:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	160 print "Open {0} error: your ngs.plot database may be corrupted.".\
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	161 format(gn_list)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	162 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	163
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	164 db_f.write("\t".join(output_order) + "\n")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	165
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	166 for k in g_tbl.viewkeys():
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	167 rec = []
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	168 for col in output_order:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	169 rec.append(str(g_tbl[k][col]))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	170 db_f.write("\t".join(rec) + "\n")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	171
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	172 db_f.close()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	173
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	174
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	175 def listgn(root_path, args):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	176 """List installed genomes in local database on screen.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	177
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	178 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	179 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	180 args: currently not used.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	181 Returns: None.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	182 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	183
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	184 import math
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	185
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	186 (h_sp, g_tbl, v_cw) = read_gnlist(root_path, "vector")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	187
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	188 # Format column widths to beautify output.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	189 tab_u = 4
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	190 v_cw = map(lambda x: int(math.ceil(float(x) / tab_u) * tab_u + 1), v_cw)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	191
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	192 # List genomes to screen.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	193 print "".join(map(lambda x, y: x.ljust(y), h_sp, v_cw)) # header.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	194 for k in sorted(g_tbl.viewkeys(), key=str.lower):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	195 print "".join(map(lambda x, y: x.ljust(y), g_tbl[k], v_cw))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	196
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	197 def isExAnno(pkg_files):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	198 """If the package is an extension package based on cell lines for ngs.plot,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	199 like enhancer or dhs.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	200
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	201 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	202 pkg_files: list of files in the package.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	203 Returns:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	204 isEx: Bool, if the package is an extension package.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	205 feature: string, feature name contained in the extension package. None
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	206 if not an extension package.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	207 RDcount: number of RData tables in the package.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	208 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	209
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	210 import os.path
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	211
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	212 exclusive_files = [".chrnames.refseq", ".chrnames.ensembl", ".metainfo"]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	213 isEx = False
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	214 RDcount = 0
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	215 feature = None
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	216 for file_name in pkg_files:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	217 if os.path.basename(file_name) in exclusive_files:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	218 continue
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	219 if (not file_name.endswith("RData")) and (file_name.count("/")) > 0:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	220 isEx = True
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	221 feature = file_name.split("/")[1]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	222 elif file_name.endswith("RData"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	223 RDcount += 1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	224 return (isEx, feature, RDcount)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	225
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	226 def install(root_path, args):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	227 """Interactive session for installing genome from package file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	228
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	229 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	230 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	231 args.yes: say yes to all questions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	232 args.pkg: path of package file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	233 Returns:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	234 None.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	235 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	236
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	237 import tarfile
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	238 import sys
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	239
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	240 yestoall = args.yes
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	241 pkg_file = args.pkg
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	242 # Package name: e.g. ngsplotdb_mm10_71_1.0.tar.gz.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	243 # Information about the genome is in mm10/.metainfo.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	244 try:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	245 pkg_f = tarfile.open(pkg_file, "r:gz")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	246 except tarfile.ReadError:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	247 print "Read package file {0} error.".format(pkg_file),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	248 print "The downloaded file may be corrupted."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	249 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	250
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	251 print "Extracting information from package...",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	252 sys.stdout.flush()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	253 pkg_files = pkg_f.getnames()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	254 g_folder = pkg_files[0]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	255 # Minus folder name and .metainfo file name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	256 (isEx, feature, RDcount) = isExAnno(pkg_files)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	257 if isEx:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	258 print feature + " extension package, ",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	259 print "contains " + str(RDcount + 2) + " tables."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	260 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	261 print "contains " + str(RDcount + 2) + " tables."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	262 # .metainfo file:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	263 # "ID"<TAB>mm10
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	264 # "Assembly"<TAB>GRCm38
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	265 # "Species"<TAB>mus_musculus
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	266 # "EnsVer"<TAB>71
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	267 # "NPVer"<TAB>1.0
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	268 meta_f = pkg_f.extractfile(g_folder + "/.metainfo")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	269 meta_tbl = {}
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	270 if meta_f:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	271 for rec in meta_f:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	272 rec_sp = rec.strip().split("\t")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	273 meta_tbl[rec_sp[0]] = rec_sp[1] # format: Variable<TAB>Value
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	274 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	275 print "No meta information found in the package file.",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	276 print "The downloaded file may be corrupted."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	277 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	278 meta_f.close()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	279 pkg_f.close()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	280
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	281 gn_inst = meta_tbl["ID"]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	282 assembly = meta_tbl["Assembly"]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	283 species = meta_tbl["Species"]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	284 ens_ver = float(meta_tbl["EnsVer"])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	285 np_ver = float(meta_tbl["NPVer"])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	286
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	287 # Database file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	288 (h_sp, g_tbl, v_cw) = read_gnlist(root_path, "hash")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	289
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	290 if gn_inst in g_tbl:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	291 installed_ens = float(g_tbl[gn_inst]["EnsVer"])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	292 installed_np = float(g_tbl[gn_inst]["NPVer"])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	293
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	294 # For extension package.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	295 # Only the same version with basic package could be installed.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	296 if isEx:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	297 if ens_ver == installed_ens and np_ver == installed_np:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	298 print "Will upgrade the genome {0} with {1} annotation:".format(gn_inst, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	299 feature),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	300 print "Ensembl: {0}; ngs.plot: {1}.".\
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	301 format(installed_ens, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	302 if yestoall:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	303 install_pkg(root_path, pkg_file, gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	304 update_gnlist(root_path, g_tbl, gn_inst, assembly, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	305 species, ens_ver, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	306 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	307 ans = raw_input("Continue?(y/n): ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	308 while True:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	309 if(ans == "y" or ans == "Y" or ans == "n" or ans == "N"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	310 break
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	311 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	312 ans = raw_input("Answer must be y/Y or n/N: ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	313 if(ans == "y" or ans == "Y"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	314 install_pkg(root_path, pkg_file, gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	315 update_gnlist(root_path, g_tbl, gn_inst, assembly, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	316 species, ens_ver, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	317 return
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	318 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	319 print "This is an extension package of " + feature + \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	320 ", ENS version " + str(ens_ver) + ", NPVer" + str(np_ver) + \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	321 ", please install the same version basic genome annotation first!"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	322 return
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	323
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	324 # For basic package.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	325 # Install a newer version.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	326 if ens_ver > installed_ens or \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	327 ens_ver == installed_ens and np_ver > installed_np:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	328 print "Will upgrade the genome {0}:".format(gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	329 print "Ensembl: {0}==>{1}; ngs.plot: {2}==>{3}.".\
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	330 format(installed_ens, ens_ver, installed_np, np_ver),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	331 if yestoall:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	332 install_pkg(root_path, pkg_file, gn_inst, gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	333 update_gnlist(root_path, g_tbl, gn_inst, assembly, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	334 species, ens_ver, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	335 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	336 ans = raw_input("Continue?(y/n): ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	337 while True:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	338 if(ans == "y" or ans == "Y" or ans == "n" or ans == "N"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	339 break
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	340 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	341 ans = raw_input("Answer must be y/Y or n/N: ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	342 if(ans == "y" or ans == "Y"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	343 install_pkg(root_path, pkg_file, gn_inst, gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	344 update_gnlist(root_path, g_tbl, gn_inst, assembly, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	345 species, ens_ver, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	346 # Install an older version.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	347 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	348 print "Will install the same or older version",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	349 print "of the genome {0}:".format(gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	350 print "Ensembl: {0}==>{1}; ngs.plot: {2}==>{3}.".\
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	351 format(installed_ens, ens_ver, installed_np, np_ver),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	352 if yestoall:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	353 install_pkg(root_path, pkg_file, gn_inst, gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	354 update_gnlist(root_path, g_tbl, gn_inst, assembly, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	355 species, ens_ver, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	356 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	357 ans = raw_input("Continue?(y/n): ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	358 while True:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	359 if(ans == "y" or ans == "Y" or ans == "n" or ans == "N"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	360 break
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	361 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	362 ans = raw_input("Answer must be y/Y or n/N: ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	363 if(ans == "y" or ans == "Y"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	364 install_pkg(root_path, pkg_file, gn_inst, gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	365 update_gnlist(root_path, g_tbl, gn_inst, assembly, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	366 species, ens_ver, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	367 # Totally new installation, only basic package could be installed.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	368 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	369 print "Will install new genome {0}:".format(gn_inst),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	370 print "Ensembl=> v{0}; ngs.plot=> v{1}.".format(ens_ver, np_ver),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	371 if yestoall:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	372 install_pkg(root_path, pkg_file, gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	373 update_gnlist(root_path, g_tbl, gn_inst, assembly, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	374 species, ens_ver, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	375 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	376 ans = raw_input("Continue?(y/n): ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	377
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	378 while True:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	379 if(ans == "y" or ans == "Y" or ans == "n" or ans == "N"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	380 break
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	381 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	382 ans = raw_input("Answer must be y/Y or n/N:")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	383 if(ans == "y" or ans == "Y"):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	384 install_pkg(root_path, pkg_file, gn_inst)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	385 update_gnlist(root_path, g_tbl, gn_inst, assembly, \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	386 species, ens_ver, np_ver)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	387
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	388
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	389 def install_pkg(root_path, pkg_file, new_gn, old_gn=None):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	390 """Install genome from package file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	391
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	392 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	393 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	394 pkg_file: package file name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	395 old_gn: old genome name to be removed first.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	396 Returns:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	397 None.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	398 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	399
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	400 import shutil
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	401 import tarfile
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	402 import sys
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	403
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	404 if old_gn:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	405 print "Removing installed genome:{0}...".format(old_gn),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	406 sys.stdout.flush()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	407 shutil.rmtree(root_path + '/database/' + old_gn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	408 rm_dbtbl(root_path, old_gn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	409 print "Done"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	410
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	411 print "Installing new genome...",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	412 sys.stdout.flush()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	413 try:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	414 tar_f = tarfile.open(pkg_file, "r:gz")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	415 except tarfile.ReadError:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	416 print "Read package file {0} error: ".format(pkg_file),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	417 print "downloaded file may be corrupted."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	418 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	419
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	420 try:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	421 tar_f.extractall(root_path + "/database")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	422 except tarfile.ExtractError:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	423 print "Extract files from package error.",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	424 print "The downloaded file may be corrupted."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	425
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	426 add_dbtbl(root_path, new_gn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	427
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	428 print "Done"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	429
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	430
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	431 def add_dbtbl(root_path, gn):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	432 """Add a new genome into database meta tables.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	433
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	434 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	435 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	436 gn: genome name to add.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	437 Returns: None.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	438 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	439
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	440 import os.path
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	441 import os
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	442 import glob
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	443 import tempfile
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	444 import subprocess
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	445
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	446 (dblist_f, dblist_n) = tempfile.mkstemp(text=True)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	447 (gnlist_f, gnlist_n) = tempfile.mkstemp(text=True)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	448
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	449 # Obtain a list of .RData file names to extract info from.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	450 all_rdata = root_path + '/database/{0}/{1}*.RData'.format(gn, gn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	451 all_set = set(map(os.path.basename, glob.glob(all_rdata)))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	452 all_rdata = root_path + '/database/{0}//{1}.RData'.format(gn, gn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	453 all_set = all_set \| set(map(os.path.basename, glob.glob(all_rdata)))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	454 exm_rdata = root_path + '/database/{0}/{1}exonmodel.RData'.format(gn, gn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	455 exm_set = set(map(os.path.basename, glob.glob(exm_rdata)))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	456 nex_list = sorted(list(all_set - exm_set))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	457
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	458 # DB file list.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	459 gn_ens_list = {} # Ensembl genome name unique list.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	460 desired_ncols = 6
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	461 for fname in nex_list:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	462 tokens = fname.split('.')
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	463 tokens = tokens[:6]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	464 if tokens[-1] == 'RData':
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	465 tokens[-1] = 'NA'
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	466 tokens.extend(['NA'] * (desired_ncols - len(tokens)))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	467 os.write(dblist_f, fname + "\t" + "\t".join(tokens) + "\n")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	468 if tokens[1] == 'ensembl':
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	469 gn_ens_list[".".join(tokens[:3])] = 1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	470 os.close(dblist_f)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	471
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	472 # Ensembl genome name list.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	473 for gn in sorted(gn_ens_list.viewkeys()):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	474 os.write(gnlist_f, gn.replace(".", "\t") + "\n")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	475 os.close(gnlist_f)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	476
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	477 # Call external program to create table default file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	478 (default_f, default_n) = tempfile.mkstemp(text=True)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	479 subprocess.call(["setTableDefaults.py", gnlist_n, default_n])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	480 os.remove(gnlist_n)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	481
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	482 # Call external program to calcualte DB score and install the new entries
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	483 # into ngs.plot database.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	484 subprocess.call(["install.db.tables.r", default_n, dblist_n])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	485 os.remove(default_n)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	486 os.remove(dblist_n)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	487
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	488
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	489 def remove(root_path, args):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	490 """Remove genome from ngs.plot database.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	491
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	492 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	493 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	494 args.yes: say yes to all questions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	495 args.gn: genome name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	496 Returns:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	497 None.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	498 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	499
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	500 import shutil
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	501 import sys
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	502
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	503 yestoall = args.yes
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	504 sub_ftr = args.ftr
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	505
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	506 (h_sp, g_tbl, v_cw) = read_gnlist(root_path, "hash")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	507
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	508 gn = args.gn
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	509
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	510 if gn in g_tbl and sub_ftr is None:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	511 print "Will remove genome {0} from database.".format(gn),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	512 do_rm = False
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	513 if yestoall:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	514 do_rm = True
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	515 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	516 ans = raw_input("Continue?(y/n): ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	517 while True:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	518 if ans == 'y' or ans == 'Y' or ans == 'n' or ans == 'N':
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	519 break
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	520 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	521 ans = raw_input("The answer must be y/Y or n/N: ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	522 if ans == 'y' or ans == 'Y':
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	523 do_rm = True
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	524 if do_rm:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	525 folder_to_rm = root_path + "/database/" + gn
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	526 print "Removing genome...",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	527 sys.stdout.flush()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	528 shutil.rmtree(folder_to_rm)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	529 del g_tbl[gn]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	530 write_gnlist(root_path, g_tbl)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	531 rm_dbtbl(root_path, gn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	532 print "Done"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	533 elif gn in g_tbl and sub_ftr is not None:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	534 print "Will remove genomic feature {0} of genome {1} from database."\
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	535 .format(sub_ftr, gn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	536 do_rm = False
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	537 if yestoall:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	538 do_rm = True
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	539 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	540 ans = raw_input("Continue?(y/n): ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	541 while True:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	542 if ans == 'y' or ans == 'Y' or ans == 'n' or ans == 'N':
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	543 break
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	544 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	545 ans = raw_input("The answer must be y/Y or n/N: ")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	546 if ans == 'y' or ans == 'Y':
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	547 do_rm = True
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	548 if do_rm:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	549 folder_to_rm = root_path + "/database/" + gn + "/" + sub_ftr
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	550 print "Removing genome...",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	551 sys.stdout.flush()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	552 shutil.rmtree(folder_to_rm)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	553 # g_tbl does't need to be updated
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	554 rm_dbtbl(root_path, gn, sub_ftr)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	555 print "Done"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	556 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	557 print "Cannot find the genome in database. Nothing was done."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	558
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	559
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	560 def rm_dbtbl(root_path, gn, sub_ftr=None):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	561 """Remove a genome from database meta tables.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	562
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	563 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	564 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	565 gn: genome name to remove.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	566 Returns: None.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	567 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	568
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	569 import subprocess
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	570
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	571 if sub_ftr is None:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	572 subprocess.call(["remove.db.tables.r", gn])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	573 else:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	574 subprocess.call(["remove.db.tables.r", gn, sub_ftr])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	575
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	576 def chrnames(root_path, args):
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	577 """List chromosome names for a given genome.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	578
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	579 Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	580 root_path: ngs.plot installation directory.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	581 args.gn: genome name to remove.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	582 args.db: database(ensembl or refseq).
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	583 Returns: None.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	584 """
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	585
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	586 import sys
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	587
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	588 db = args.db
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	589 gn = args.gn
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	590
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	591 if db != "ensembl" and db != "refseq":
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	592 print "Unrecognized database name: database must be ensembl or refseq."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	593 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	594
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	595 chrnames_file = root_path + "/database/" + gn + "/.chrnames." + db
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	596
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	597 try:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	598 chrf = open(chrnames_file)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	599 except IOError:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	600 print "Open file: {0} error.".format(chrnames_file),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	601 print "Your database may be corrupted or you have an older version."
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	602 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	603
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	604 chr_list = chrf.read(1000000) # set 1MB limit to avoid nasty input.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	605 chrf.close()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	606
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	607 chr_list = chr_list.strip()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	608 print chr_list
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	609
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	610
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	611
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	612 ###############################################
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	613 ######## Main procedure. ######################
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	614 if __name__ == "__main__":
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	615
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	616 import argparse
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	617 import os
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	618 import sys
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	619
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	620 try:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	621 root_path = os.environ["NGSPLOT"]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	622 except KeyError:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	623 print "Environmental variable NGSPLOT is not set! Exit.\n"
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	624 sys.exit()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	625
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	626 # Main parser.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	627 parser = argparse.ArgumentParser(description="Manipulate ngs.plot's \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	628 annotation database",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	629 prog="ngsplotdb.py")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	630 parser.add_argument("-y", "--yes", help="Say yes to all prompted questions",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	631 action="store_true")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	632
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	633 subparsers = parser.add_subparsers(title="Subcommands",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	634 help="additional help")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	635
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	636 # ngsplotdb.py list parser.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	637 parser_list = subparsers.add_parser("list", help="List genomes installed \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	638 in database")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	639 parser_list.set_defaults(func=listgn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	640
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	641 # ngsplotdb.py install parser.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	642 parser_install = subparsers.add_parser("install",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	643 help="Install genome from package \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	644 file")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	645 parser_install.add_argument("pkg", help="Package file(.tar.gz) to install",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	646 type=str)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	647 parser_install.set_defaults(func=install)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	648
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	649 # ngsplotdb.py remove parser.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	650 parser_remove = subparsers.add_parser("remove",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	651 help="Remove genome from database")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	652 parser_remove.add_argument("gn", help="Name of genome to be \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	653 removed(e.g. hg18)", type=str)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	654 parser_remove.add_argument("--ftr", help="Remove cellline specific features \
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	655 (enhancer, dhs, etc)", type=str,\
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	656 default=None)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	657 parser_remove.set_defaults(func=remove)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	658
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	659 # ngsplotdb.py chromosome names parser.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	660 parser_chrnames = subparsers.add_parser("chrnames",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	661 help="List chromosome names")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	662 parser_chrnames.add_argument("gn", help="Genome name(e.g. mm9)", type=str)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	663 parser_chrnames.add_argument("db", help="Database(ensembl or refseq)",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	664 type=str)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	665 parser_chrnames.set_defaults(func=chrnames)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	666
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	667
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	668 args = parser.parse_args()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	669 args.func(root_path, args)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	670

Mercurial > repos > artbio > ngsplot

annotate bin/ngsplotdb.py @ 2:4b4d858c0aa9 draft