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Various fixes in fasta tools.

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This commit is contained in:
Greg Von Kuster
2008-04-25 14:49:40 +00:00
parent 5657e61320
commit 9cd868d779
4 changed files with 82 additions and 84 deletions
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tools/fasta_tools/fasta_compute_length.py
+25 -33
View File
@@ -7,46 +7,38 @@ Return sequences whose lengths are within the range.
import sys, os
seq_hash = {}
def parse_fasta_format(file_handle):
tmp_title = ''
tmp_seq = ''
tmp_seq_count = 0
for i, each_line in enumerate(file_handle):
each_line = each_line.rstrip('\r\n')
if (each_line[0] == '>'):
if (len(tmp_seq) > 0):
tmp_seq_count += 1
seq_hash[(tmp_seq_count, tmp_title)] = tmp_seq
tmp_title = each_line
tmp_seq = ''
else:
tmp_seq = tmp_seq + each_line
if (each_line.split()[0].isdigit()):
tmp_seq = tmp_seq + ' '
if (len(tmp_seq) > 0):
seq_hash[(tmp_seq_count, tmp_title)] = tmp_seq
return 0
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
input_filename = sys.argv[1]
output_filename = sys.argv[2]
tmp_title = tmp_seq = ''
tmp_seq_count = 0
seq_hash = {}
for i, line in enumerate( file( input_filename ) ):
line = line.rstrip( '\r\n' )
if not line or line.startswith( '#' ):
continue
if line[0] == '>':
if len( tmp_seq ) > 0:
tmp_seq_count += 1
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
tmp_title = line
tmp_seq = ''
else:
tmp_seq = "%s%s" % ( tmp_seq, line )
if line.split()[0].isdigit():
tmp_seq = "%s " % tmp_seq
if len( tmp_seq ) > 0:
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
input_handle = open(input_filename, 'r')
parse_fasta_format(input_handle)
input_handle.close()
output_handle = open(output_filename, 'w')
title_keys = seq_hash.keys()
title_keys.sort()
for (i, fasta_title) in title_keys:
tmp_seq = seq_hash[(i, fasta_title)]
print >> output_handle, "%s\t%d" %(fasta_title[1:], len(tmp_seq))
output_handle = open( output_filename, 'w' )
for i, fasta_title in title_keys:
tmp_seq = seq_hash[ ( i, fasta_title ) ]
output_handle.write( "%s\t%d\n" % ( fasta_title[ 1: ], len( tmp_seq ) ) )
output_handle.close()
return 0
if __name__ == "__main__" : __main__()
tools/fasta_tools/fasta_filter_by_length.py
+46 -41
View File
@@ -7,64 +7,69 @@ Return sequences whose lengths are within the range.
import sys, os
seq_hash = {}
assert sys.version_info[:2] >= ( 2, 4 )
def parse_fasta_format(file_handle):
tmp_title = ''
tmp_seq = ''
tmp_seq_count = 0
for i, each_line in enumerate(file_handle):
each_line = each_line.rstrip('\r\n')
if (each_line[0] == '>'):
if (len(tmp_seq) > 0):
tmp_seq_count += 1
seq_hash[(tmp_seq_count, tmp_title)] = tmp_seq
tmp_title = each_line
tmp_seq = ''
else:
tmp_seq = tmp_seq + each_line
if (each_line.split()[0].isdigit()):
tmp_seq = tmp_seq + ' '
if (len(tmp_seq) > 0):
seq_hash[(tmp_seq_count, tmp_title)] = tmp_seq
return 0
def stop_err( msg ):
sys.stderr.write( msg )
sys.exit()
def __main__():
input_filename = sys.argv[1]
min_length = int(sys.argv[2])
max_length = int(sys.argv[3])
try:
min_length = int( sys.argv[2] )
except:
stop_err( "Minimal length of the return sequence requires a numerical value." )
try:
max_length = int( sys.argv[3] )
except:
stop_err( "Maximum length of the return sequence requires a numerical value." )
output_filename = sys.argv[4]
tmp_title = tmp_seq = ''
tmp_seq_count = 0
seq_hash = {}
for i, line in enumerate( file( input_filename ) ):
line = line.rstrip( '\r\n' )
if not line or line.startswith( '#' ):
continue
if line[0] == '>':
if len( tmp_seq ) > 0:
tmp_seq_count += 1
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
tmp_title = line
tmp_seq = ''
else:
tmp_seq = "%s%s" % ( tmp_seq, line )
if line.split()[0].isdigit():
tmp_seq = "%s " % tmp_seq
if len( tmp_seq ) > 0:
seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq
input_handle = open(input_filename, 'r')
parse_fasta_format(input_handle)
input_handle.close()
output_handle = open(output_filename, 'w')
title_keys = seq_hash.keys()
title_keys.sort()
output_handle = open( output_filename, 'w' )
at_least_one = 0
for (i, fasta_title) in title_keys:
tmp_seq = seq_hash[(i, fasta_title)]
if (max_length <= 0):
compare_max_length = len(tmp_seq)+1
for i, fasta_title in title_keys:
tmp_seq = seq_hash[ ( i, fasta_title ) ]
if max_length <= 0:
compare_max_length = len( tmp_seq ) + 1
else:
compare_max_length = max_length
if (len(tmp_seq) >= min_length and len(tmp_seq) <= compare_max_length):
compare_max_length = max_length
l = len( tmp_seq )
if l >= min_length and l <= compare_max_length:
at_least_one += 1
print >> output_handle, "%s" %fasta_title
l = len(tmp_seq)
output_handle.write( "%s\n" % fasta_title )
c = 0
s = tmp_seq
while c < l:
b = min( c + 50, l )
print >> output_handle, s[c:b]
output_handle.write( "%s\n" % s[ c:b ] )
c = b
if at_least_one == 0: print >> sys.stdout, "There is no sequence that falls within your range."
output_handle.close()
return 0
if at_least_one == 0:
print "There is no sequence that falls within your range."
if __name__ == "__main__" : __main__()
tools/fasta_tools/fasta_filter_by_length.xml
+4 -4
View File
@@ -4,7 +4,7 @@
<inputs>
<param name="input" type="data" format="fasta" label="Fasta file"/>
<param name="min_length" type="integer" size="15" value="0" label="Minimal length of the return sequence" />
<param name="max_length" type="integer" size="15" value="0" label="Maximal length of the return sequence" help="no limitation if 0"/>
<param name="max_length" type="integer" size="15" value="0" label="Maximum length of the return sequence" help="no limitation if 0"/>
</inputs>
<outputs>
<data name="output" format="fasta"/>
@@ -21,13 +21,13 @@
.. class:: infomark
**TIP**. If only want to show sequences longer than a threshold, set *minimal length* to the threshold and leave *maximal length* to zero.
**TIP**. If only want to show sequences longer than a threshold, set *minimal length* to the threshold and leave *maximum length* to zero.
-----
**What it does**
This tool accepts two parameters: *minimal length* and *maximal length*, and returns sequences of length within the two thresholds.
This tool accepts two parameters: *minimal length* and *maximum length*, and returns sequences of length within the two thresholds.
-----
@@ -44,7 +44,7 @@
&gt;seq4
ATGGAAGC
- return sequences with length longer than 10bp (set the *minimal length* to 10, and the *maximal length* to 0 (no limitation))::
- return sequences with length longer than 10bp (set the *minimal length* to 10, and the *maximum length* to 0 (no limitation))::
&gt;seq1
TCATTTAATGAC
tools/fasta_tools/fasta_to_tabular.py
+7 -6
View File
@@ -18,6 +18,8 @@ def __main__():
sequence_count = 0
for i, line in enumerate( open( infile ) ):
line = line.rstrip( '\r\n' )
if not line or line.startswith( '#' ):
continue
if line.startswith( '>' ):
if sequence:
sequence_count += 1
@@ -25,19 +27,18 @@ def __main__():
title = line
sequence = ''
else:
if line:
sequence += line
if line.split()[0].isdigit():
sequence += ' '
sequence = "%s%s" % ( sequence, line )
if line.split()[0].isdigit():
sequence += ' '
if sequence:
seq_hash[( sequence_count, title )] = sequence
# return only those lengths are in the range
out = open( outfile, 'w' )
title_keys = seq_hash.keys()
title_keys.sort()
out = open( outfile, 'w' )
for i, fasta_title in title_keys:
sequence = seq_hash[( i, fasta_title )]
print >> out, "%s\t%s" %( fasta_title, sequence )
out.write( "%s\t%s\n" %( fasta_title, sequence ) )
out.close()
if __name__ == "__main__" : __main__()