mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Corrected the problems and updated some test data files for sniff.py
This commit is contained in:
Greg Von Kuster
@@ -5,7 +5,6 @@ import logging, sys, os, csv, tempfile, shutil, re
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log = logging.getLogger(__name__)
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valid_strand = ['+', '-', '.']
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valid_frame = [0, 2, '.']
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def get_test_fname(fname):
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"""Returns test data filename"""
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@@ -151,27 +150,32 @@ def is_gff(headers):
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>>> is_fasta(headers)
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False
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>>> fname = get_test_fname('test.gff')
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>>> headers = get_headers(fname,sep=' ')
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>>> headers = get_headers(fname,sep='\\t')
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>>> is_gff(headers)
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True
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"""
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try:
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if len(headers) < 2:
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return False
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"""
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Assume the first line in the file is not actual data
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(it could be a description), so we'll use the 2nd line
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"""
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line = headers[1]
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if len(line) != 9:
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return False
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try:
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map(int, [line[3], line[4], line[5]])
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except:
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return False
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score = int(line[5])
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if (score < 0 or score > 1000) and line[6] not in valid_strand and line[7] not in valid_frame:
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if len(headers) < 2:
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return False
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for idx, hdr in enumerate(headers):
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if hdr and len(hdr) > 1 and not hdr[0].startswith('#'):
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if len(hdr) != 9:
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return False
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try:
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map(int, [hdr[3], hdr[4]])
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except:
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return False
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if hdr[5] != '.':
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try:
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score = int(hdr[5])
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except:
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return False
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if (score < 0 or score > 1000):
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return False
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if hdr[6] not in valid_strand:
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return False
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if idx > 29:
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break
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return True
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except:
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return False
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@@ -295,9 +299,6 @@ def is_wiggle(headers):
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if hdr and hdr[0] == 'track' and hdr[1].startswith('type=wiggle'):
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return True
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if idx > 29:
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"""
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This is a weakness since it assumes < 29 blank lines, comments, etc.
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"""
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break
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return False
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except:
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@@ -317,23 +318,21 @@ def is_bed(headers, skip=1):
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>>> headers = get_headers(fname, sep='\\t')
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>>> is_bed(headers)
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True
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>>> fname = get_test_fname('interval.bed')
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>>> headers = get_headers(fname, sep='\\t')
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>>> is_bed(headers)
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False
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True
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"""
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try:
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if not headers:
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return False
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for hdr in headers[skip:-1]:
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"""
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We'll try to ensure we are not looking at a comment line
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"""
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for hdr in headers[skip:]:
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if len(hdr) < 3:
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return False
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if hdr[0].startswith('chr') or hdr[0].startswith('scaffold'):
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if len(hdr) < 3:
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return False
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try:
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map(int, [hdr[1], hdr[2]])
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except:
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@@ -388,11 +387,10 @@ def is_interval(headers, skip=1):
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the format is_column_based, but not any of the other formats, then it must be interval.
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>>> fname = get_test_fname('test_space.bed')
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>>> headers = get_headers(fname, sep=' ')
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>>> headers = get_headers(fname, sep='\\t')
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>>> is_interval(headers)
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False
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>>> fname = get_test_fname('interval.bed')
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>>> fname = get_test_fname('interval.interval')
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>>> headers = get_headers(fname, sep='\\t')
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>>> is_interval(headers)
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True
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@@ -404,13 +402,11 @@ def is_interval(headers, skip=1):
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If we got here, we already know the file is_column_based and is not bed,
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so we'll just look for some valid data.
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"""
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for hdr in headers[skip:-1]:
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"""
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This is a weakness in that it assumes no more than 5 blank lines, comments, etc.
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"""
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for hdr in headers[skip:]:
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if len(hdr) < 3:
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return False
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if hdr[0].startswith('chr') or hdr[0].startswith('scaffold'):
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if len(hdr) < 3:
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return False
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try:
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map(int, [hdr[1], hdr[2]])
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except:
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@@ -449,35 +445,33 @@ def guess_ext(fname):
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Returns an extension that can be used in the datatype factory to
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generate a data for the 'fname' file
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>>> fname = get_test_fname('interval.bed')
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>>> fname = get_test_fname('interval.interval')
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>>> guess_ext(fname)
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'interval'
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>>> fname = get_test_fname('interval.bed')
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>>> guess_ext(fname)
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'bed'
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>>> fname = get_test_fname('test_tab.bed')
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>>> guess_ext(fname)
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'bed'
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>>> fname = get_test_fname('sequence.maf')
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>>> guess_ext(fname)
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'maf'
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>>> fname = get_test_fname('sequence.fasta')
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>>> guess_ext(fname)
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'fasta'
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>>> fname = get_test_fname('file.html')
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>>> guess_ext(fname)
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'html'
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>>> fname = get_test_fname('temp.txt')
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>>> file(fname, 'wt').write("a 2\\nc 1")
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>>> guess_ext(fname)
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'tabular'
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>>> fname = get_test_fname('temp.txt')
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>>> file(fname, 'wt').write("a 1 2 x\\nb 3 4 y")
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>>> guess_ext(fname)
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'bed'
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>>> fname = get_test_fname('test.gff')
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>>> guess_ext(fname)
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'gff'
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"""
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try:
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"""
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@@ -506,7 +500,7 @@ def guess_ext(fname):
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return 'html'
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elif is_axt(headers):
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return 'axt'
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# convert space to tabs
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if is_column_based(fname, sep=' '):
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sep2tabs(fname)
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@@ -0,0 +1,74 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
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<HTML>
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<HEAD>
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<META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1">
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<META http-equiv="Content-Script-Type" content="text/javascript">
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<META HTTP-EQUIV="Pragma" CONTENT="no-cache">
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<META HTTP-EQUIV="Expires" CONTENT="-1">
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<TITLE>
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Hyperlinks to Genome Browser </TITLE>
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<LINK REL="STYLESHEET" HREF="/style/HGStyle.css">
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</HEAD>
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<BODY BGCOLOR="#FFF9D2" LINK="0000CC" VLINK="#330066" ALINK="#6600FF">
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<A NAME="TOP"></A>
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<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%">
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<!-- +++++++++++++++++++++ HOTLINKS BAR +++++++++++++++++++ -->
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<TR><TD COLSPAN=3 HEIGHT=40 >
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<table bgcolor="#000000" cellpadding="1" cellspacing="1" width="100%%" height="27">
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<tr bgcolor="#2636D1"><td valign="middle">
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<table BORDER=0 CELLSPACING=0 CELLPADDING=0 bgcolor="#2636D1" height="24"><TR>
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<TD VALIGN="middle"><font color="#89A1DE">
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<A HREF="/index.html?org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">
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Home</A>
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<A HREF="/cgi-bin/hgGateway?org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">
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Genomes</A>
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<A HREF="/cgi-bin/hgTracks?org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">
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Genome Browser</A>
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<A HREF="/cgi-bin/hgBlat?command=start&org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar"> Blat</A>
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<A HREF="/cgi-bin/hgTables?org=Bushbaby&db=otoGar1&hgsid=1118408&hgta_doMainPage=1" class="topbar">
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Tables</A>
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<A HREF="/cgi-bin/hgNear?org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">
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Gene Sorter</A>
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<A HREF="/cgi-bin/hgSession?org=Bushbaby&db=otoGar1&hgsid=1118408&hgS_doMainPage=1" class="topbar">Session</A>
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<A HREF="/FAQ/" class="topbar">
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FAQ</A>
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<A HREF="/goldenPath/help/hgTablesHelp.html"
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class="topbar">
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Help</A>
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</font></TD>
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</TR></TABLE>
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</TD></TR></TABLE>
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</TD></TR>
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<!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->
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<TR><TD COLSPAN=3>
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<!--outer table is for border purposes-->
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<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD>
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<TABLE BGCOLOR="#FFFEE8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD>
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<TABLE BGCOLOR="#D9E4F8" BACKGROUND="/images/hr.gif" WIDTH="100%"><TR><TD>
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<FONT SIZE="4"><b>
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Hyperlinks to Genome Browser</b></FONT></TD></TR></TABLE>
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<TABLE BGCOLOR="#FFFEE8" WIDTH="100%" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR>
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<TR><TD WIDTH=10> </TD><TD>
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<A HREF="http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1&position=scaffold_0.1-193456:96554-98437&gold=pack" TARGET=_blank>scaffold_0.1-193456_25 at scaffold_0.1-193456:96554-98437</A><BR>
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<A HREF="http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1&position=scaffold_0.1-193456:100227-101729&gold=pack" TARGET=_blank>scaffold_0.1-193456_26 at scaffold_0.1-193456:100227-101729</A><BR>
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<A HREF="http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1&position=scaffold_0.1-193456:101830-103994&gold=pack" TARGET=_blank>scaffold_0.1-193456_27 at scaffold_0.1-193456:101830-103994</A><BR>
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<A HREF="http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1&position=scaffold_0.1-193456:105267-107614&gold=pack" TARGET=_blank>scaffold_0.1-193456_28 at scaffold_0.1-193456:105267-107614</A><BR>
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</TD><TD WIDTH=15></TD></TR></TABLE>
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<br></TD></TR></TABLE>
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</TD></TR></TABLE>
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</TD></TR></TABLE>
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</BODY></HTML>
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@@ -0,0 +1,5 @@
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chr1 4348187 4348589 3.70 4.90 2.55 0.24 0.46
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chr1 4488177 4488442 4.03 5.77 1.92 -0.67 0.81
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chr1 4774091 4774440 8.07 8.33 7.82 0.85 -0.40
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chr1 4800122 4800409 6.40 7.35 5.44 1.19 -0.42
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chr1 4878925 4879277 2.18 0.28 4.93 -0.96 1.24
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@@ -1,3 +1,3 @@
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track name="tb_knownGene" description="table browser query on knownGene" visibility=3 url=
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track type=wiggle_0 name="tb_knownGene" description="table browser query on knownGene" visibility=3 url=
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chr7 127475281 127491632 NM_000230 0 + 127486022 127488767 0 3 29,172,3225, 0,10713,13126,
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chr7 127486011 127488900 D49487 0 + 127486022 127488767 0 2 155,490, 0,2399,
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